engine swap

Will a VQ35DE from a 01 pathfinder fit and bolt up to a 00 X with the VG33E and 5 speed tranny?

No

Unless you mean with work to MAKE it work, etc

work to make it work. i know a guy that can make me a bell housing adapter plate. but will the fly wheel be to big for the bel housing?

The mating of the bell housing will of course be different anyway, so your fly wheel will also need to take into account the required spin momentum and resulting diameter and thickness - which of course will potentially change your pilot/throwout situation, and so forth.

For example, my bell housing was a little different, so the STARTER COG no longer lined up with flywheel, and I had to machine an adapter to bring the cog back against the flywheel, etc...

IE: When you move one thing, there is a potential cascade reaction of associated parts that are also now not aligned with each other.

You'll need to methodically line things up, see what works and what doesn't, and come up with the most streamlined solution.

thank you...