In my experience of buying used cars it's not "stock" or "modded" it's "does the owner keep records?" I'd be far more wary of modded cars. Just because someone took the time and effort to personalize their car doesn't mean they did it right! But if you have records, receipts, and service histories, you know the owner has taken good care of their car and you know EXACTLY when service items were done.

Case in point, I did end up buying the VX I kicked this thread off with. It had 140,000 miles on it and the diff and transfer case fluids had NEVER been changed. The diff oil was like river water. Very, very thin, and very, very dirty. I flushed both diffs and the transfer case (twice with the t-case) and most of my drivetrain noises disappeared. I also swapped the spark plugs, which were so old they had actually rusted to the cylinder head. I'm pretty sure they were also original. I got immediate improvements in gas mileage and acceleration.

Point is, stock or modded, if the old owner(s) is lazy, cheap, or incompetent, you're going to have problems no matter what used car you're shopping for.