I've often wondered the same thing, My 94 has a thin bead, it's a little tougher than silicone but it's not hard either and it does have some stretch. I have oem hoses and clamps and I've had the bike since 20k and the first owner did not admitt to bottom end work. Top end has had work, it runs strong, smooth and dry. I had a 99 and it did not have any visable sealant.

D

 

You need to use Permatex Ultra grey Rigid High-Torque RTV Silicone Item #82194. You need to drill a .035" hole in the end of the applicator, and run one bead all the way around on one side only 1/3 the way in from the outer edge and around all the bolt holes. It is really hard to squeeze the silicone through this little hole, so have patience!!!!Allow it to dry all day and overnight. The next AM inspect it and carefully remove any that squeezed inside with a pick and some grease to pick up any pieces. Hope this helps.

 

Have you done a compression and leak down test yet???? How is that primary chain, a loose or bad chain will cause some funky vibrations as will a loose clutch or compensator sprocket. Hope this helps.

 

SE-3 Cam, milled heads, SE air cleaner,
I did check compression, it was 175# even on both cylinders engine cold.
The primary chain was at 3/4 " cold.
The front mount had the threads stripped out on the bottom hole (alum)
So I will replace it this week end, the mount looked good, I put a lomger 3/8
bolt in it and rode it but no change.
The timing was so far advanced the dot was out of sight, I had to retard
it two (large lines) on the plate but it did not make any difference.
I listened with a scope on the primary but did not hear any strange noises
other than a light rumble sound (not loud) by the clutch.
Thanks

 

Permatex Moto seal(grey).