The 8.8 is a very good option. Lots of support for it both for the drag racing crowd, Mustang owners, and of course for the off-road community. You should be fine with an 8.8.
Shortage of d44s?? Not around my area (Southern Indiana near Louisville KY). If you want something that bolts in I understand you can find d44s under some '86-'87 Cherokees and they reportedly bolt in directly. I'd like to hear from someone on here that has performed this swap first hand so I can stop going off what I read and be more comfortable offering up this as gospel.