Couple of Q's
I was wondering how far the pilot bearing goes into the engine. Will it just go as far as possible or will it keep going and do you need a special tool.

And what kind of sealant do you use to reseal the flywheel nut

 

Don't use any sealant. Just use a torque wrench and tighten to the correct torque.

The pilot bearing will eventually stop, if I remember correctly.