From my research, I'd have to ask how much are you willing to spend on the swap. Alot of the manual swaps are going to require an adapter ring to the Dana 300 transfer case. Those sometimes ain't cheap. If you had to also get an adapter for the I6, you're into the swap some pretty significant money. The only bright spot I can think of is that with a TC adapter, you could also clock the TC and install a flat transmission/TC skid plate.
Another question is why are you moving away from the T5? It's lasted the last 25 years. I'm sure since September you didn't rebuild it and the problem has gotten worse. Another alternative is to get a T5 Rebuild Kit and rebuild the existing transmission. At first, this may seem a waste of money; however follow my logic for a while.
Rebuilding the T5 will be among the least expensive alternatives, with kits running about $250. It's something you could do over a week-end, or so. Then you'd have the Jeep back on the road again, that's worth something. Since the Jeep's driving up and down the road, and it's reliable, you could then pick your poison (so to speak) and get the transmission you want. Then get the adapters at your leisure. You'd not be rushed as the Jeeps broken down sitting there rusting. You'd have time to plan your work and work your plan. When you're done with the swap, if it's in a reasonable amount of time and within a few thousand miles of the rebuild, you could also recoup your cost in the rebuild kit by selling the T5. That beats throwing it away at a boneyard or selling it for scrap.
I don't see you swapping the T5 for any other manual for anything less than about $800, and that's with a used transmission. This is a serious chunk of change to drop on an "experiment." I don't care how much the guy you buy the tranny from swears it's "like new." Buyer Beware!
Until you pick a transmission and know your costs, I'd think twice about dumping the T5.