Well, here they are - all my secrets!  Really they aren't secrets, just things I've tried and know that they work.  I hope some of these modifications are usefull for you.

Water Pump:

The late model 4.0L H.O. (91 – present) water pump is made of aluminum and utilizes an improved impeller design for increased water flow rate.  The pulley bolt pattern is unchanged from the earlier AMC sixes, but the shaft length is shorter, the pump turns in reverse compared to the standard pump, and the large radiator connection is at the 5:00 position instead of the standard 2:00 position., which may interfere with some accessories.

The Moroso water pump drive may be used to drive the water pump for drag race applications; attach it with the timing cover bolts on the distributor side of the engine.  It can be wired to run clockwise or counterclockwise, allowing it to operate the reverse rotation water pumps if needed.
 

Thermostat:

Balanced, high-flow thermostats are available from Robertshaw in 160 and 180 degree opening points.  I use the 160 degree thermostat with a 2-core stock radiator, but would recommend 180 minimum for most street/strip vehicles.  Mr. Gasket also offers balanced, high-flow units in 160 (part #4363), 180 (part #4364) and 195 (part #4365) degree opening points.  The Mr. Gasket ones are identical to those offered by Robertshaw.  Nothing less than 195 degrees should be used on daily driven vehicles in order to minimize condensation buildup inside the engine and keep contaminants vaporized, allowing them to vent.  The above listed part numbers also can be used on slow, heavy, inefficient, high heat-generating V8’s.
 

Timing Chain:

Cloyes offers a “True Roller” dual-roller timing chain and gear set for the AMC six.  The crank gear has three keyways, allowing you to advance or retard the cam by 2 degrees.  This chain and gear set is superior to all I have seen, and after thousands of street miles and hundreds of ¼ mile passes the chain is still as tight as the day I bought it.  A replacement chain is available for this set.  The stock oil slinger may not be used with a dual-roller timing chain set.
 

Carburetion:

I’ve used two basic carbs, both Holleys.   The general Holley 4-bbl. sizes best suited to this application are the 390, 450, and 600 cfm carbs.  The 600 cfm should be used in vacuum secondary configuration only. Also popular are the 350 and 500 cfm 2-bbl. carburetors, although I feel that more precise mixture control is possible when using a 4-bbl. carb.  I install a Ford-type automatic kickdown throttle shaft in all of my Holley’s to run the A904’s kickdown.  A new linkage rod between the carb and transmission must be fabricated.

390 cfm- Although many people use a 390 cfm vacuum secondary carburetor, I feel that it presents too large a restriction at low rpm before the secondaries open.  I have used a 390 cfm HP series double-pumper (#80157) with some success.  For drag race use, the tunability of four-corner idle, and homogenity of mixture delivered by a symmetrical bore carburetor are hard to beat.  The throttle butterfly plates must be replaced with those from a standard 390 cfm carburetor to eliminate the holes found in those of an HP series carb.  An air cleaner stud must be installed in the HP series carburetor at all times due to the stud hole being drilled completely through the carb body, or a massive vacuum leak will exist.

450 cfm – I have not used this size carburetor, although it would appear to be an excellent choice.

600 cfm – I have done most of my racing with 600 cfm vacuum secondary carburetors.  Many people feel that the 600 cfm carb is too large, but my experience is that the car will go faster when the secondaries of these carbs are allowed to open relatively quickly.  Tuning one to work well on the AMC six takes some finesse, but is well worth the trouble.  My basic setup is as follows:
     Ford-style automatic kickdown throttle shaft.
     Quick-change secondary spring kit.
     Purple secondary spring.
     Moroso clear bowl sight plugs.
     Holley secondary metering block kit (or 4160 carb to start with).
     Size 67 primary jets.
     Size 70 secondary jets.
     8.5 primary power valve.
     Holley hollow accelerator pump shooter screw.
     Size 41 accelerator pump shooter (tube type).
     50cc accelerator pump system.
     Orange pump cam on position 2  (yes, I am using the wrong cam for the 50cc accelerator pump).
Further gains can be realized by replacing the primary booster venturis with annular discharge booster venturis.  The resulting increase in low RPM booster signal allows a minor reduction in main jet and accelerator pump nozzle size.  This modification can be performed by any of the specialty carburetor shops, including The Carb Shop and Holley Custom Shop.
 

Fuel Pump:

The stock pump (with or without vacuum pump) is inadequate for high performance use.  The easiest solution is to use a Holley electric pump.  The Holley “Blue” pump with regulator will provide more than enough capacity for racing use even with nitrous power augmentation.  A big block Chevy fuel pump block-off plate will fit in place of the AMC six cylinder pump and can be purchased from sources such as Mr. Gasket.
 

Air Filter:

Always use an air filter, and never use any air filter other than K&N.  K&N filters have been proven to flow more air than any other filter, and filter as effectively. Two 14" K&N drop base (required to clear the hood on my Javelin) air cleaners are available, but only part number 60-1440 (7/8" drop) will clear a stock height valvecover when using a Clifford intake manifold and Holley 4-bbl.  NEVER run the engine without an air filter.  Your ring seal will suffer and power will drop, mandating a rebuild.  Many carbs flow more air with an air cleaner installed, and typically mixture quality is improved.
 

Thermal Barriers / Surface Finishes:
 
I have used Tech Line ceramic coatings on valves and combustion chambers with good results.  Adhesion is excellent when the surface is prepared per their recommendations, which involves sandblasting.  For standard forged or cast pistons, their ceramic coating will improve thermal efficiency and increase piston life.  For hypereutectic pistons, a thermal barrier coating applied after sandblasting will reduce piston strength due to the increase in surface area created by the sandblasting.  Hypereutectic pistons have excellent insulating properties, and the only improvement I (and John Erb, Chief Engineer at KB/Silvolite) recommend is to polish the piston tops to increase reflectivity and decrease surface area.
 

Harmonic Balancer:

Felpro offers a chrome plated repair sleeve for the harmonic balancer.  Cool the balancer in the freezer for a day and heat the sleeve in hot water, then dry it off and quickly install it using red or blue locktite.  Use of this sleeve and a new front seal will eliminate front seal leaks.
 

Spark Plugs:

Avoid Split-Fire sparks plugs – my back-to-back test passes indicated a loss of 0.020 seconds in the quarter mile due to these plugs vs. standard Champion plugs.  Standard style Champion plugs have been shown to exhibit the longest spark burn time for the lowest spark energy of any other plug.  If you must use a glorified spark plug of some sort, use the Champion Gold.  I gap my plugs at 0.045” with the stock GM HEI, and at 0.050” with the GM HEI coupled to a MSD 6AL.  I have seen the MSD generate a spark of over ½”.  Use a minimum of one heat range colder plug for every 100 additional horsepower above stock.  I use Champion RN12YC, which is two heat ranges colder than the stock RN14YC.  There is also an extended tip version available you may want to experiment with.
 

Plug Wires

I always use a quality spiral core wire like that made by Taylor or Accel.  Taylor has custom fit sets available for 6 cylinders with HEI boots; I use Taylor because they are located here in Kansas City and I like to support the local economy when I can.  Avoid solid core (they interfere with electronics) and Split-Fire plug wires (I hope it’s obvious why).  In order to minimize inductive crossfire related problems, do not route any wires parallel and close together.  Keep all spark plug wires as far apart from each other and from anything metal (block, head, etc.) as you can – Smokey recommends ½” spacing between these items as a minimum.
 

Head Gaskets:

I've used two different head gaskets.  I like the Felpro gasket best (Felpro 8196PT), and have had no failures with them.  Felpro 8169PT measures 0.050" thick at the fire ring and the fire ring inside diameter is 3.875", resulting in a gasket volume of 9.7 cc.  I have also used a gasket from Victor which had a 0.042" thick fire ring (8.1 cc gasket volume), but I did experience a head gasket failure.  I always attempt to re-torque the head after the initial run-in period and before I expose the engine to wide open throttle conditions, but with the ARP bolts and the Felpro gasket I have been finding that none is required.
 

Crankshafts:

I've run in to two different 258 cranks so far.  Casting 3214723 appears to be the most popular, and I've seen it in both 1975 and 1980 model year engines.  Casting 3188947 is the early (1971 model year) 258 crank that was used with the last of the Borg Warner transmissions, and therefore has a smaller pilot hole in it for the converter.  It won't work with the Torqueflite without some machining, so I avoid them.  I remove the casting flash on my crankshafts with a die grinder before they are reground in order to reduce the tendency for oil to attach to them.  I have not attempted knife-edging or pin drilling on one of these cranks, though it should be possible and beneficial.  My cranks are always ground 0.010-0.010, oil holes are chamfered, and journals are micro-polished.  The crank should be set up in the block after machining to check main journal runout with a dial indication.  With the block upside down, insert the bearing shells for the bearings on either side of the journal you are checking, oil them, and set the crank in place.  Set up a dial indicator and ensure the runout is less than 0.001".  Note that you can't just toss in the #1 and #7 bearing shells and check all the other runouts; the crank will sag under it's own weight and give inaccurate readings.  When the crank is ground properly and the block has been align honed you will be able to freely spin the crank when completely installed and oiled (no rods, pistons, or rear main seal) with two fingers.  If this is not the case, something is wrong and the clearances should be re-checked.
 

Balancing:

The AMC six is internally balanced.  All inline six cylinders are balanced without bob-weights due to the design of the crankshaft throws.  This allows all components to be balanced separately.  Pistons and rods are scale balanced, and the crank, flexplate/flywheel, and harmonic balancer are spin balanced.  You can change any component of the rotating assembly as long as it is re-balanced to match the other existing parts.  Even after removal of casting flash, the 258 crankshafts typically require little balance adjustment from the factory balance job.
 

Camshafts/Springs/Retainers/Lifters:

I use a mild Crane hydraulic cam (part #753941) with the following specs:  Duration@0.050"=216/228, Advertised duration=272/284, Lift@1.6=.484/.512, LC=112.  My rocker ratio is effectively 1.75:1 therefore I end up with lift numbers of around .529/.560.  Although it doesn't appear that way from the numbers, this cam is extremely streetable, idles well, produces excellent low end torque, and maintains very good idle vacuum.  The reason for these many qualities is the low overlap resulting from the 112 degree lobe center angle.  Even with all the above listed qualities, I still run in the 13's with the camshaft.

The only problem I have had with the camshaft is that it builds too much cylinder pressure in my 11:1 motor, and therefore the starter has a hard time cranking the engine.  For my purposes, a camshaft of 284/292 degree duration with a slightly tighter lobe center of maybe 110 degrees would build more top end power (remember, my converter stalls around 3000).  Ultradyne is rumored to be able to grind custom cams for the AMC six, and has also publicized their ability to grind special cams for 0.900" lifters (which AMC's and Chryslers use).  The large diameter lifter permits increased cam lobe ramp rates without wear problems, resulting in increased off-seat duration and lift rates (more "area under the curve") and hence more flow without increasing advertised duration.  The Chevy guys can't do this, and most cam companies base all their grinds of what works for a Chevy.

The springs, retainers, and lifters I'm using are those recommended by Crane for this cam.  Part numbers are: Springs = 99838-12, Retainers = 99948-12, Lifters = 99278-12.  All have performed flawlessly.  One note here though - the springs have a very large diameter that barely clears the valvecover.
 

Oil Pans:

Oil pans are different between the 199/232 engines and the 258.  The 258 pan has 6 protrusions on the drivers side to provide clearance for the connecting rods on the 258's long stroke crankshaft.  I learned this the hard way, and as a result I have a very nice 199/232 pan for sale complete with screen, scraper and baffle (if you are interested).  I baffle the sump of the pan using sheet metal equal to the pan thickness.  The baffle is installed at the same height as the front floor of the pan, and includes a few radius edged drain holes to allow oil to drain easily (but not slosh through them) and a hole just big enough to get the oil pump pickup through.  The baffle fits tight to the back of the pan to prevent oil from climbing up to the crank on drag racing launches.  I use a Moroso universal windage screen trimmed to clear the oil pump and connecting rods, and spaced up from the pan floor with 1/8" bar stock to permit easy drainback to the sump.  The last item I install could be called a scraper, but in actuality a scraper that fits tight to the crank can not be used on the passenger side of these engines because it would direct all oil dropping from the head and the cam right into the crank, defeating the purpose.  Instead it helps create a pocket on the side of the pan that acts more as a "kick-out" to catch slinging oil from the crank.  The scraper rail must get a notch to allow the dipstick in to the oil pan.