O man where to start! Ary, you got your self into a pickle here
There was a post a few months back about using gears from a Toyota Supra in the AX-15. The AX-15 is related to the Supra tranny because of the manifacture Asian Warner which came with a lower first gear and a taller 5th gear or something like that. I cant remember the exact details but the cost of changing the gearing inside the tranny was outragious so I didnt both pursuing it farther.
As for the axle gearing in relation to the tranny gearing, I have Bridgestone Dueller A/Ts in the 32x11.50 flavor and 4.10s. At 80mph or so I am just under 3,000rpm. It doesnt feel like the motor is going to blow up or anything. No need to down shift to pass people unlis you really want to get around them in a hurry. I usually cruse at 70 to 75mph and the rpms are around 2500 to 2800.
Since you are a speed demon you should really consider getting an intake, t-body, header, and full exhaust. You would be surprised how well these mods will work in the accerlation department. If you want to go for a little bit more, add a cam and FEEL the power

Thats basically what I did but with a few more mods
Driving with the manual offroad will take all sorts of finess. Its very difficult to rock crawl with it so be warned. I like the challenge of the manual offroading when compared to an auto but again each person to his own
Now for the swap:
1. Tranny of your choice, AX-15 or NV3500. I would go with one of these just for cost and ease of swapability. They are both Jeep trannys that came in the XJ stock. Try and get the tranny with a bell housing. Stay away from 93 and older AX-15. They have the crapy internal slave cylinder. 94 and newer AX-15s and the NV3500 have external slaves.
2. Use the flywheel for the same year as your Jeep. You have a 2001 right? SO use a flywheel out of a 2001 XJ. Theres issues with crank position sensor if you try and use a different flywheel. I dont know about the later models but I screwed up and used the flywheel out of my 89 doner Jeep in my 91 and couldnt get the engine to fire because of the different CPS thing.
3. Computer-Again for the newer Jeeps, I believe the auto tranny is controlled by the ECU and not a seperate computer so you may have issues with the ECU seeing that there is not an auto tranny attached. You may have to change to a manual tranny ECU. There will be some wireing issues and you will just have to figure them out with the factory manual or just cut and see what happens.
4.Shifter: Pull out that auto shifter and toss it! You will have to make a custom cover for the hole left by the auto shifter. The manual tranny hole is very small when compared to the auto. This is no big deal, just a small piece of sheet metal.
5. Clutch and petals: You should be able to look way up on the fire wall and see 3 punch marks. The center punch mark is for the plunger of the master cylinder and the top and bottom punch mark is for the mounting bolts. Remove the auto brake petal and install the clutch and brake petal assymbly from a manual equiped XJ. Try and take all parts from the same year Jeep as yours. DC made all sorts of small weird changes that will throw the absolutly biggest monkey wrench you have ever seen into your project.
I am sure that there is some stuff that I have left out or gotten wrong so point it out and I can fix it.
Good Luck
AARON
EDIT: Had to add some stuff