Motorcycle Repair: Inner Primary Leak, shaft seal, swing arm

Question
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Followup To
Question -
I have a 1990 Fat Boy, stock, with 21,000 miles and have never had any problems with it.  Other than regular maintenance the motor, primary, and tranny have never been touched.  It has never leaked.  This spring we took a break after riding a while and I noticed a leak from the rear primary area.  I thought that the drain plug was not tight and tightened it. That did not solve the problem.  It is most noticible when you come to a stop and while putting the bike in neutral or holding the clutch in it dumps a small puddle of fluid.  It seems to only do it after the bike gets hot.  Once you park, it will drip for a while and then stop.  You can tell that it leaks while riding since the fluid is on the swing arm and rear tire.  It got worse and finally I removed the innner primary.  All indications were that the mainshaft seal was leaking. The transmission seal was dry.  I replaced the mainshaft seal and the jackshaft seal and put everything back together per specs.  I have the HD repair manual and followed it.  However, once I took it for a test ride, the same thing happened.  While I had the inner primary off, I cleaned it and did not notice any cracks but I did not check it real close.  I'm begining to think that I have a cracked inner primary.  What do you think?  I would appreciate any advice you can give me.
Answer -
do you install the prinary and jack shaft seal correctly?.
is it leaking from the back of the inner primary ?. Johnny
602-705-7474

Yes the seals were installed correctly as far as I know.  I was careful to remember how they came out and I also referred to the diagrams in the manual.  The answer to your second question is yes.  it is leaking from the back of the inner primary.  it is wet as far up as I can reach with my hand towards the mainshaft.  

Answer
you could of tore the seal if you did not tape up the main shaft before installing the inner primary. this is really hard to fix over the computor my friend, It seams like you covered all bases from what you said. do not use silicone anywhere, If you are to use anything to seal the primary use Yamaha Bond Grey.  Johnny