Crankshaft Seals

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Cranshaft seal sizes:
Front Seal:  25mm x 62mm x 10mm
Rear Seal:   35mm x 62mm x 10mm
These are both commonly available from any good industrial bearing and seal supplier.  Simply ask for them by size.
This little adventure began when the engine became hard to start.
Following the complete engine rebuild, which included having the crankshaft rebuilt, this engine fired up with just a blip of the key.  However, after a couple trips to the lake, it was becoming more and more difficult to start, especially when hot.  The other thing I was experiencing was a very inconsistant idle, where previously, it would idle nice and low without issue.  Now it would only idle above about 2,000rpm and if it died, it would only restart after putting in a cold set of plugs.
The hard starting finally became "no" starting, which of course was a great motivator to pull the engine and dig into the problem.
I started with some simple ohm's tests on the ignition system to see if there were any obvious problems with the 2 external ignition coils (mounted on the mag end of the cylinder block), or their spark plug wires. 
Right off I discovered that one plug wire had an infinite amount of resistance.  These were new copper core wires and new old stock "Bombardier" plug wire ends.   I removed the wire and retested the coil.  It tested good.  I then tested the plug wire with the end still on.  Infinate.  I removed the end and discovered that when I had screwed the end onto the plug wire, the little screw "spike" down inside the plug wire end had been canted off to one side.  This made it go into the plug wire at an angle barely touching any of the copper strands inside.  I cut this damaged end off the wire, screwed the plug wire end back into place and that solved the problem.
From here I went to check the ignition timing, again using my digital meter.  The timing was way off and it seemed the points weren't really doing a good job of "switching" from closed to "open."   I removed the flywheel and sanded the contacts of both sets of points and then did more resistance tests. 
This actually helped the readings greatly, but the timing was still way out, even though I'd just set the points to .012" gap.  The timing mark was literally 1/4" or more to the right of the timing mark on the ignition housing.  I knew there was no way a points gap adjustment, or even a stator plate movement was going to take care of this discrepancy!
This was my first of many mistakes in attempting to solve this problem.  The points gap listed in the Sea Doo shop manual that I have clearly shows .014"-.018".  I quickly learned that setting the points to .018" would get the timing marks nearly perfect with the stator plate in the middle of its adjustment slots.
When I put it all back together and into the Sea Doo, it still wouldn't start.  I then disconnected the engine's harness where it plugs into the Sea Doo's harness, part of which goes to the ignition key as a kill switch.  Guess what?  It fired right up with the pull starter!
So, now I had it running, but it wouldn't idle down low without dying, and it wouldn't take any amount of throttle opening, especially if I rolled on the throttle fast.  It would instantly die....sort of a bogging.... and if I let up on the throttle and it would immediately recover begin running again. 
Also, if I shut it off, or let it stumble at idle and die, it would not restart until I either let the engine sit for hours, or put in another set of spark plugs.  The plugs I'm using are brand new NGK A-7's with no run time on them, so it wasn't like I was using old fouled plugs.
Once I got it fired back up, I sprayed starting fluid on the rear crankshaft seal.  This killed the engine within a few seconds!  Guess what?  My new crankshaft seal was bad, with only about 5hrs on it!
I'm awaiting the arrival of new seals and will update once they're installed.
I installed the new pto seal, reinstalled the engine and it wouldn't start at all.  I barely got it running once, and it again wouldn't take throttle, died and that was it.   I was wrench throwing mad at this point.
However, calmer minds prevail and I have to give a big pat on the back to Dan Fairchild of Fairchild Performance in Michigan.  Dan's a very talented 2 stroke machinist, a darn good wrench, and an excellent diagnostician.  He's been a great friend and has been very patient in offering advice over the phone and via email.
When I was talking about breaking out the Sawzall, Dan was talking about, "I think you should do a pressure test on the engine and see if you have a leak somewhere."
Like a buddy and very talented mechanic friend of mine used to say, "Who's smarter?  You, or the car?"
Anyway, back to the story:
I pulled the engine back out.  Removed the carb and cut some thick rubber-like gasket material to fit over the carb bolt flange/intake opening.  Then I bolted the carb back on.  Then I put some thick plastic over the end of the exhaust pipe and taped it down good with clear packing tape.  I slipped a long fuel hose onto the water pipe that goes into the end of the exhaust pipe and began simply blowing through it with my mouth. 
As fast as I could blow in, I could hear air hissing out of the engine somewhere.  I narrowed down the area to be somewhere around the drain plug for the mag side of the crankcase.  I couldn't see anything, so I used some of my daughter's bubble wand liquid soap on the area and watched for bubbles when I blew.
Sure enough, there it was, a hole in the case where the boss for the mag side drain meets the curvature of the case.  It was some sort of casting flaw I guess, but it was about 1/8" in diameter.
I gracefully packed in a wad of the epoxy putty steel, like you see on the counter in many autoparts stores.  You know, the dark grey stuff that has a penny and bolt bedded into it.  That stuff is fantastic and I use it all the time.  5 minutes later, it was dry and I could pump the case up with my Stant Coolant System Pressure Tester to 9psi.  Then, I put my Might Vac on and sucked the case down to 20" of vacuum.  It was now nice and tight.
I put the engine back in and it would fire up, run for a bit, but then flood out and die.  It still wouldn't take any throttle either.  I kept pulling the crankcase drains and getting a bunch of fuel/oil mix just running out.  Even with the carb's needles turned all the way in (off) I was still getting fuel.
I pulled the carb off and took the fuel pump assembly off the bottom.  It looked like it had been in with the Titanic for the last week! 
I'd just rebuilt this carb in January so I was shocked to see it all rusty and cruddy inside.  The needle and actuating arm were seized with rust in the open position.....hence the flooding.  The check ball in the high speed jet was seized and the jet was blocked.....hence the no taking any amount of throttle!
With the carb all cleaned and back in place the engine fired right up, even on the electric starter, and ran perfect.  It would take any amount of throttle and idle nice and low!
The following day, I added a squeeze bulb to the fuel line just before the carb.  Now on that first cold start, I can reach in, give the bulb a squeeze or two, pull the choke and hit the key.
Now, a brief note about the water I'm getting in my fuel.  The fuel tank vent, located on the right side of the bow, just below the chrome intake air scoop, is positioned so that it gets nailed every time the bow gets hit with a wave.  This is especially pronounced if I do a spinout.
I think the key to alleviating this is to install a new vent hose, and position it so it makes a tall upside down "U" shape up into the top of the bow and then back down to the fuel tank.  This will still vent the tank, but it will keep water that enters from running down into the tank.
We took the Sea Doo to the lake the day after completing these repairs.  The check ball in the carb was still hanging up and I had to smack the carb body with a screwdriver handle to break it loose and get the engine to take throttle.  Once it was loose again, the engine ran super and really made some great power.  We had a good ride, with excellent acceleration, and top speed.  Probably the best and fastest it's ever run!  However, after about 45min. of riding, the mag side cylinder quit firing and we limped into the marina and came home.
So far all I've had time to do is diagnose that it's a failure of either the top set of points, the condensor attached to them, or the magneto that powers them.  I'll provide another update once I take the engine out AGAIN!!!!!!!
Thanks for reading this long winded story and I hope some of it becomes useful, even if only when printed out and used to line the bird cage or wrap fish.