there have been a few people inthe last while ask this very question. it has been agreed on that a stock TJ would be a better purchase then a modified TJ. even if you spend a little more for a good condition stock unit.
odds are if it does have a lift, tires and bumpers it wont be the ones that you may like. and they will be worn or low end parts.
but, if you come across a litghtly modified Tj, then a proper inspection could score you a deal on a good starter jeep.
each situation will be different. like Fiend said, there are a bunch of techs that could do front to back inspections to see if a "good deal" really is a good deal.
good luck:)