-is there anything relatively cheap that i should go ahead and replace while everything is pulled?
Certainly. Do a full tune-up on the new engine. Replace any and all filters (air, fuel, oil) and all the spark plugs and plug wires. New dizzy cap and rotor are good ideas too. All of this stuff together should be under $100.
-are their any other engine/transmission combos i should know about before putting in another ax-5/amc engine?
Certainly. The Chevy smallblock 350 EFI / 4L6E auto trans combo out of a Chevy Tahoe and similar are proven swaps and are well-suited for our Jeeps. If you want a manual trans, go with a Borg-Warner T18 or T19; they're heavy-duty, quite strong, and very plentiful. You will need adapters to bolt them up to your transfer case and etc. and you can get these adapters from Novak or Advance Adapters.
-is it true that i could go with a v6 with a carburetor and not have to worry about wiring/computer issues?
The first thing I'll say is ... don't go with a V6 unless it's a really good, really powerful V6 to begin with. Otherwise, it won't be worth the time/trouble/money you will have invested. If you're gonna do a swap, save yourself the hassle and do it right the first time -- just go to a V8.
Now, for your real question ... that depends on the design of the carb, really. There were some odd carbs in the past that were electronically controlled to an extent (although these are quite rare) and there's always throttle-body injection, which is kinda like a carb, but all electronic. Still, you'll probably be safe. But if you're gonna do an engine swap you'll probably have to go EFI unless you can find a 1992 or newer V6 that was carb'd. Most states have laws that require engine swaps to be same year as the target vehicle or newer. Definitely check your local state's laws. Don't just Google them, call your local DMV. It's not a big deal to go EFI, really; just make sure you pull the ECU and TCM (if you're going automatic) and the wiring harness from the swap engine's donor vehicle.
-is there anything i could do for a little bit more speed on the interstate if i do go with the 2.5L?
Yep. You can swap to a larger Throttle Body for starters. A stock 4.0L TB has a larger bore than a stock 2.5L TB and is a good low-cost choice, they run around $25 in junkyards. There are also various performance TB's available that have bores up to 64mm but you will need to grind out your intake inlet a bit for these to give you any gain over a 4.0L TB.
A 3" diameter snorkel or cold air intake also helps, especially when matched with a larger TB.
High flow performance exhaust systems are available for the 2.5L and are always a good option for some extra oomph.
If you go to one of the performance TB's you can consider upgrading to bigger injectors and getting an adjustable fuel pressure regulator so you can richen out the mix and send more fuel to the cylinders. When working in conjunction with a bigger TB and a larger intake, this can make a very noticeable difference. A wideband O2 kit with an air/fuel ratio gauge would be recommended for tuning this; you don't want to run too lean by accident and frag your engine via detonation, and on the flip side, running too rich can kill your gas mileage as well as your power. Jeeps already run slightly lean from the factory, so more air without more fuel makes it run even leaner; you want to keep the mix as close to stoic as possible, and you need these tools to do that properly.
One more excellent option is the E-Fan swap. Basically you take an electric fan out of a 3.8L Ford Taurus of certain years and replace your mechanical fan with it. Then you buy a ramp-up box from Delta Control so it doesn't kill your alternator when the fans engage. The low-speed circuit is more than enough for our 2.5L's. There are quite a few write-ups on this over at 4bangerjp.com, and I recommend you check em' out sometime. This will not add horsepower but it will free up a few ponies that were already being used to turn the mechanical fan all the time.
There are also some performance cams available but I honestly know nothing about them.
The big one is regearing your axles. This comes with a high price, though; it can cost upwards of $1000 to regear both your axles, and if you were gonna do it, you wouldn't want to spend that money on the stock D35 rear axle.
With all of these mods together (minus the e-fan swap and regearing) you might be able to pull another 20-30hp out of those four angry squirrels. But in the grand scheme of things, that's a pittance when you look at the money invested to perform all of these upgrades. It should get you doing 80mph on the highway in 5th gear on flat road, though.
If you wanted to get really serious you could go forced induction. There are a few guys doing forced induction setups on 4bangerjp, you could take a look at what they're doing and see if you like what you hear.
Sure. I hope I helped you in some way. Don't take everything I said as set in stone; I implore you to do your own research and talk to many people before you commit to your swap.
