My bike has developed a leak from the tranny side cover. It is probably from taking a shortcut during the removal and installation of the tranny cover without removing the exhaust.This time I plan to do it right and take the exhaust off, replace the tranny gasket and torque it properly.

Remember there are no dumb questions, only dumb________ so here goes.

The bottom two threaded holes (marked with red arrows) usually get filled with tranny oil when you open the cover. Is it necessary to make sure that there is no oil in these threaded holes? What do you use to clean it?

I know I'm gonna get flamed for asking but oh well that's one way to learn.

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Yes if you are going to use lock tight or some junk. Brake cleaner & some q-tips would clean it out nicely. I would also get new screws for the cover in case the leak was cause from stretched out hardware.

 

I think it would be best to remove the oil as stated above.
Its possible the cover was leaking becuase the bolts were not tightened correctly.
I would reuse the bolts.

 

I would think just a new gasket would be sufficient. Reuse, clean and tighten the existing bolts according to the shop manual. I don't think the torque value is significant enough to cause stretching or thread damage, even after several torqueings. I haven't used gasket seal on mine, but if you feel better with it, be vary sparing. Just enough to cover the gasket on both sides with a film.