I think if you want to put bigger tires, a lift or use it offroad at all you should keep looking for a 6 cylinder.
unless you have plans for a motor swap?
I disagree. Do you have experience with a 4 cylinder to make such claims?
To the OP, if it's nice and clean and you like the way it drives, go for it! If you're looking to lift it, 4.88 gears will help a lot in the power department. 4.88's, 33's and a 5 speed would be a very nice setup. You'll be able to do 75-80 on the highway (though it will be a bit slow getting up to speed).
upgearing is great, but unless you have the tools/know how to do it yourself the price you'll pay for an upgear is the difference it would cost to get into a 6 in the first place. and yes, I've had a 4cyl yj... in fact I've had two and two other 6 cyl yj's. if I had the choice I'd get a motor that doesn't fall on it's face in the torque department.
now, in an effort to remain humble, if it makes you happy then go ahead and get it. I know a few guys that wheel 4 bangers and while they all want to do a swap in the long run, they are all happy with them.
Jeep: Pioneered by a war, popularized by AMC, revived by Chrysler, jacked by some Germans, and copied by all.
I am a newb to jeeps, I have 4cyl 2000 TJ 5 spd. How do you go about completing that gear set up of 4.88 you were talking about?
You should take it to a shop and have them do it. It's something you don't want to mess with if you don't have experience. I would call some local shops for quotes.
To the other posters, yes, the cost of a regear could be added to the budget towards a 4.0L TJ but even a 4.0L on 33's (especially since many have 3.07 gears) will need a regear so that point is sorta mute.
I agree, if you can afford it, get a 4.0L. If you do happen to find a nice 2.5L though, don't be afraid to get it.