If starting from a clean sheet of paper, a 6 cylinder of any kind would not be on my build sheet but it depends on what the actual expectations are for the completed project. There aren't any more inherent problems with V8's versus 6's and they are certainly more pleasurable to drive both on and off road. And they CAN get the same mileage.
Transmission? Auto or manual? Personal preference as there are several of each that work well.
Axles? The AMC 20 would be one that I would not use but depending on use, D44's can work well and there are a lot of more robust options. Wheel spacers would not be on my build sheet either.
The best advice one can give is to start doing some research. Novak Adapters has a lot of good information on their site and I would do some reading at some of the more CJ orientated sites:
Early CJ5.net > Forums
Then, with your specific use in mind, put together a specific plan for the drivetrain, steering, and brakes. At that point you could post it and get some useful feedback.