All good questions to ask, and the answers do exist here somewhere.
The AX-15 is longer than the automatic, and the floor hump under the driver side will need some modification with a big hammer at least. I may revisit my postponed swap soon, and I will be addressing making more clearance by pulling the interior to modify the floor hump to allow the 242 I have swapped in to tuck further up under the car.
I fabricated a new transmission crossmember to handle using an XJ transmission mount. I do not care for how low the mount I made hangs beneath the car, and plan to redo it completely.
I used the Girling/Eagle/Jaguar remote reservoir master cylinder. Clearance around the vacuum brake booster on the Eagle firewall does not leave enough room to use a Jeep master cylinder. The factory Eagle master cylinder, made by the British company Girling, was shared with some Jaguar cars of the late 70s, and I think I was able to buy a new master cylinder reservoir from Pegasus Auto Racing, and it came with AN fitting provisions. Really, any reservoir, including those from motorcycles, can be made to work as a proper reservoir to the only master cylinder that fits the Eagle firewall - the factory cylinder.
The Jeep external slave cylinder is plastic, and has a strange pinned & o-ring connection to the plastic hysraulic line. Advance Adapters sells a brass fitting that converts this strange connection to an AN fitting, size 3, if I recall. They also sell threaded AN adapters for the master cyl end, and braided stainless hydraulic hose long enough to make the trip between the master and slave. If you hate the idea of a plastic slave cylinder, like I do, Advance Auto carries the Perfection brand line, and part number 360047 is made from aluminum. I disassembled the aluminum slave I bought and drilled the bleed screw hole for a standard bleed screw and tapped an existing small weep port on the side of the bleed port to plug it, giving the slave an true bleed port. Seems complicated, but the Jeep clutch hydraulic system was never intended to be serviceable as anything more than a complete, pre-bled system.
I have chosen to use a Jeep starter to match the Jeep flywheel, clutch assembly, and throwout bearing. The AMC flywheel is thicker, and will result in a clutch that does not engage, like permanent neutral. The jeep starter has an integrated solenoid, so there is some wire rearranging to be done if you choose to eliminate the Ford solenoid used in the Eagle factory wiring.
Also, there are different grades of clutch kits out there, and some contain a plastic throwout bearing carrier. I bought a LUK clutch kit, but I recall buying a separate throwout bearing with a cast iron carrier. I have a strong dislike for plastic parts in hard to reach places.
Finally, there is a very important retainer clip for the throwout fork, keeping it on its pivot ball. Do not leave out this $2 clip, the throwout fork will fall off of the pivot and bad things happen inside the bellhousing after that. I have not had it happen to me, but I have seen the results of leaving the clip off on another person's Jeep.