Does anyone know if a stock 400ex transmission will hold up, if I turn the motor into a 465 stroker? And should I be aware of any other problems that could occur?

 

My brother in law did a 460 stroker on his 400ex and he didnt have any problems with his transmission and he rode it ***** to the wall.

 

Depends on what you bump the compression up to, then you need to worry about the bottom end.
I've seen many times where the compression was bumped up so much that you'd blow out the head gasket or the main bearings.
As long as you stay close to stock compression, you shouldn't have a problem.