Man. I'm out in Phelan and I wish I could help. If you were doing YJ drivetrain stuff I might be able to. lol. Although the front driveshaft should be simple. Could just be a matter of getting new u-joints to match the new t-case. And you should be able to use the existing fuel rails, just plumb them from the tank and then to the FI on the motor with the correct fittings.
If your t-case has a slip yolk eliminator already, you don't modify the rear drive shaft you buy a new one. Try here http://www.4xshaft.com/
really good company.
Edit: I was browsing the other site and noticed you have the tank up for free. Is it the plastic one?