In any defender, 90 or 110, you want to check out the outriggers and rear crossmember, the outriggers go and need replacing, however if your going to build it to your own spec you may strip it down to the chassis and be able to replace these, so thats not a great problem, but worth looking for a good chassis.
Check the bulkhead, this should be fairly solid, they do rust so you can expect a bit, but if its got holes all over it, then its going to need replaced, again if your rebuilding and the price is right, you will be able to replace this easily enough.
Check the engine and running gear, make sure the gears all engage ok, and that the transfer box works. There should be no excessive play in the prop shafts, get under and give them a twist, they can also be heard as clunks when taking off, slowing down, gear changing etc...
The engine, does it start well, run smoothly, if its got blue smoke pouring out the exhaust chances are the rings are worn, turbo knackered etc... so could be an engine rebuild job costly parts replacement. Black smoke; fuel problems etc...
90 = SWB
110 = LWB