I just purchased a 2006 trx350 from an auction.
It is missing the jug, head, carb, basicly the whole top end.
I was wondering if a trx400 top end would bolt up to the trx350 bottem end?
If not, anyone got any ideas where I could get a good used 350 top end?

 

Those engines only share a design, but not any parts. Even if you could adapt the cylinder from the 400 to the 350, there would still be challenges you couldnt overcome without redesigning the entire top end.
Check around on Ebay for starters.
After that, make a few calls to your local dealers. Not for new parts, but to check with the shop for borable cylinders and rebuildable heads. Honda doesnt always call this stuff back after a warranty claim and so the parts are usually stored for salvage pieces.
Also there are salvage yards with online forms for inquiries as to what you are looking for.