I also have the infamous 0331 head. No issue so far at 106k. Just like you I'm not overly concerned.00 and 01 models have the 0331 head, which is prone to cracking. Most don't, but enough do that it's a known problem. Didn't stop me from buying my 2000 5-speed Sahara, which had my favorite color scheme of any TJ—green with tan interior—but I monitor my coolant like a hawk. I can get a TUPY head for $450, so not too concerned. Other years have their problems, too, from cracking exhaust manifolds on 97-99, OPDA on 05 and 06, potentially overblown PCM problems on auto 05 and 06s. Generally, if you want a manual, avoid the 6-speed on the 05 and 06; it's a total dog. The 3-speed auto before 2003 is probably the best transmission, but the 4-speed is serviceable as long as you keep it cool.
Get what ever year TJ you can find in the best condition with the lowest price. If you're going to do a lot of rock crawling get an auto. If you plan on going off road a lot spend a bit extra now and get a Rubicon so you can save some money down the road. Also, if you're looking for a non Rubicon check to see if it has a dana 44.