I wish the Atlas 4 would fit better. I really wanted one, but it just seems very difficult. You can get it shorter by not running a speedometer signal from the tcase. I've got an extended fuel tank, so I can't massage the thing in too much.
If you went with a smaller fuel tank, maybe you could get yourself a couple of inches with your suspension setup, but I don't know. Personally I just decided to go Atlas 2 after I get my axles swapped out and add a locker. I'm going to try and see if I can still get the 6:1 tcase, but 5:1 wouldn't be bad either.
I've been trying to look into regearing the AX-15, but I haven't seen definitively how to successfully do that. There is supposed to be a way to get a 1st gear of ~4.1 and ~5.15. My engine is different, but 1-3 from the AX-15 aren't exactly what I'd want in a perfect world. If I could get a major granny gear and then a second gear close to what the current 1st gear is and then a slightly higher (2nd vs the AX-15 3rd) that would be my preference. That would let me take off in second without using the accelerator pedal and would remove a shift that doesn't do a lot for me in general. I think even with the 4.0 a different transmission similar to the Marlin 515 ( I think) would be a nice addition to most manual TJ owners.
On the other hand, a future build I want to do will be to take a wrecked YJ I have and stretch it and I'm going to try and to a doubler with NP-231 and Dana 300 (4:1) which would be ideal imo in a bunch of scenarios, but similar to the Atlas 4 in gearing. No idea if I can actually couple those 2 or not, but I thought I saw it done somewhere. Part of me wants to go for broke on that thing and get a TR-4050 with ~6.15:1 first gear, so 4.1x6.15x10.88.