I don't have direct experience, but I did an engine and clutch swap on a 6 cylinder SUV before. It was more modern so there were a LOT more things to pull of the engine before it could be removed. Either way, if I was going to do just a clutch swap I'd strongly consider pulling the transfer case and transmission from below. You'd want to get the vehicle up as high as you safely can - I'd put it on 4 jack stands and get a creeper. If the CJs are the same as the SUV I did, the engine / transmission bolts thread in the from the transmission side - the tops were a PITA to get at. I used a 2 foot long ratchet extension, and one or two swivels. I was wrenching the thing from back by the exhaust, but it made it a lot easier to have a somewhat straight shot in.
You need the right kind of (transmission) jack to lower the parts out without dropping them on you - it's harder to manage than using an engine lift to pull up on an engine. I chained my transmission around a normal small-footprint floor jack and it was sketchy at best. I'd buy the right tool this time.
This would have pros and cons. On the downside, you have to work entirely from under the vehicle. On the upside, you don't have to unhook anything from the engine compartment. It seems like a CJ would be a lot easier than a modern vehicle but I bet the radiator would still need to come out. (I pulled my SUV engine out through the middle of the AC lines because I didn't want to drain them and refill. It was a total pain, and I wore a face mask and thick gloves in case I busted a line...)
This might sound like a joke, but if you decide to go from underneath, start doing crunches and head lifts in your spare time. Your back and neck will hate you otherwise.