I personally own the 4-banger, and here is what I have done to mine (and some things I have not yet done, but I am actually exploring):
First step; reduce the power load on the engine!
1. eFan conversion: I used a Ford Taurus fan, and run it through a Delta Current Control box, which adjust the speed of the fan automatically dependingon the tempreature of the radiator. This will not MAKE horsepower, but will free up some power used by the mechanical fan. It is one of the best conversions.
2. I have not done this myself, but I have read that the FlowKool water pump actually uses LESS power than the stock pump and has better flow. Be careful if you havethe stock radiator, though, as this one has plastic tanks on the sides, and more pressure could cause the radiator to go BOOM!
Improve the air/fuel mixture:
2. Mustang 19# injectors. These will not only allow more fuel to go in, but actually have 4 nozzles instead of the one the stock injectors have. Your stock ECU will be able to manage the new injectors quite well (you just need to cycle the computer about 50 times for it to "learn")
3. Performance Distributors Ignitions; they sell a pack including their screaming demo coil, livewires, rotor and cap. By using this kit, you can gap your plugs at .065 instead of the .035 that's stock, which means you will have better combustion in your engine.
Now you have more fuel and better spark; you need mor oxygen to get a good mix...
4. High Flow filter; the paper element is restrictive, so I go with higher flow ones; I used to run a K&N in the stoc box, but it was letting some dirt into the engine, so I switched to the FRAM Airhog (besides, there was a promo in Amazon that actually made the filter free!). I removed the 2 restrictors from the stock airbox (one on the intake of the airbox, and the other is on the outgoing tube), but I did not feel any difference in my but-dyno.
5. 62mm Throttle Body and spacer; since this will allow more air to flow into your combustion chamber, and you have now the potential for more fuel and better spark, it will just complete the triangle... Talk to Bounty Hunter about this one, I know he sells them. The biggest difference here you will feel on you but-dyno when it comes to throttle response; it will be much more crisp...
6. Colder air; I know some people have actually taken CAI setups OUT of their 4-banger because it hurts low-end performance, so careful what you choose. Personally, I run a Safari Snorkel, so although technically I dont have a CAI, the snorkel doe in fact act as one.
Now that you have improved combustion, you need to get all that OUT of the engine...
7. Start with a good cat-back system. I have run both Gibson and now Borla, and they both work fine (Borla is much more expensive, but it is also stainless steel; only reason I switched is that my cat blew up and ruined the Gibson, but it had nothing to do with the cat-back itself).
8. Consider a hih flow cat; I personally run a CarSound by Magnaflow, but a clogged up cat can kill the performance of the engine... I only changed mine because the old one blew up (that was the result of a coil dying on me; long story that I can tell you some other time...), so I moved up to the high-flow ones when I had to change it anyway...
9. Headers; personally, I run the stock ones, but let me warn you that not all aftermarket headers are desireable; some are designed for max HP, but you want low-end torque. Be sure that your choice will not sacrifice the torque for hi-RPM horse power (which you will rarely use, to be hones!).
Now, I have to tell you, I am currently running 31" tires, and with the stock motor, I had to downshift to 4th at highway speeds if there was any incline (and keep in mind that I live in Miami, where it is FLAT, so by incline, I mean an overpass!) or any headwinds. By doing all this mods, the little 4-banger did better, but not as good as it is now that I regeared to 4.88 on both axles... In your case, you hvethe stock tires, so you should not need to regear, but if you are thinking about larger tires, consider that with 33" and all these mods, the Jeep will run about the same as you have now...
If you want more information about people that have put Turbos, Superchargers, bored blocks, increased compression, etc. I recommend you drop by
www.4bangersjp.com and read a bit. That site is exlcusively dedicated to 4 cylinder Jeeps, and there is A LOT of information there about how to improve the 4-banger with people that have actually done the mods themselves.
Anyway, sorry about the LOOOOONG reply, but I hope it helps!
Felipe