Sean,
I haven't been on here in a while, I wish I had caught this thread at the beginning. Here's some of my advice after daily driving/owning a '98 TJ Wrangler for a year:
Buying considerations:
I4 vs I6:
I have the 4 banger and it really doesn't bother me. The only time I ever wish I had the I6 was driving through Colorado and having to downshift to 3rd on some gnarly passes.
For off-roading, engine size is almost trivial. If something is too steep for 4-Hi, then I drop it into 4-Lo and make quick work of it. Like Ben said, tire size should be your main consideration for engine size.
Tranny:
Simply a matter of preference. You already drive stick, I think having manual jeep adds to the experience.
Other stuff:
There are a lot of stupid Jeep owners out there that do stupid stupid mods. When searching to buy, try to find one on the lower end of your price range that is close to stock. You'll get to build it up yourself and it's really rewarding. Every time I work on my jeep I find something stupid the previous owner did. Try to avoid this by buying from a Jeep owner who is older and possibly selling to buy another Jeep; search forum classifieds.
After you bought it:
Wait to mod it. Go off-roading with it a few times and then you'll know exactly what you want to do with it. Find out if you like rock crawling, mudding, hill climbing or whatever. I jumped right into modding my jeep and since I'm on a limited budget, I haven't done things that I wish I had done in retrospect.
Let me know if you want to go off-roading sometime. I'll even let ya drive.
