There is a list of items for the 2" and taller lifts on the 3rd gen install page (I e-mailed this to you earlier today):
http://www.4Crawler.com/4x4/ForSale/....shtml#Updates
Generally 2" has no big issues on the 3rd gens, aside from access to the spare tire winch.
Also, it is hard to give absolute answers regarding what issues you may run into with various height body lifts. There seems to be a fair amount of variations in the way the vehicles are assembled, so while some folks have no issues at 2", while some have problems at 1". Others will have minimal issues at 3" while other find more things to fix up at 2". Also varies with vehicle types, a Tacoma is usually harder to fit a given lift on than a 3rd gen 4Runner, for example. So basically all the possible things one might run into are addressed on the installation page; not that any one person will run into everything listed.