The best lift for a YJ can be argued a lot but if boils down to what you want to run and use the rig for.
With a SOA setup you can definitely run large tires without a problem, but in the 5-6 range, and good set of SUA springs can definitely compete with a SOA setup. With 37s, you probably would need to go to a SOA setup because you will need the height, unless you get happy with a sawzall. SOA with stock height springs should be more than enough and maybe some cutting or a 1" BL
As for the axle swap it really depends on the vehicle they are going into. You mentioned YJ, TJ, and XJ. For a YJ waggy axles are very popular because they are a pretty easy swap. The D44 and 8.8 with handle the tires but the front you are pushing your luck. If you stick with a D44 or 8.8, a rubi front axle would be the best bet as if would be a direct swap for a TJ or XJ. With a D44/9" setup you will run into problems with the width, but this might not be a problem.