Given what you said, I'd carefully check the fuel supply line and fuel return line going forward from the gas tank. It may be that you bent or crimped one of those lines when you lowered the transfer case. Check the lines all the way forward, not just where they go past the t-case. Since the drivetrain is now tilted, check to insure that the fuel supply/return lines from the engine aren't now hitting the frame of the vehicle. Also, if you jacked up the vehicle when working on the t-case, you may have crimped a line with the head of the jack.

1977 CJ-7, fiberglass body, AMC 360 w/ headers, DUI ignition, Edelbrock intake and Holley 4150 carb, TF999, Dana 300, 4.56 gears lockers, York air comp, 4" susp lift, 2" body lift, BFG 35" M-T tires, Megashifter, AGR pump & box, REP8000 winch.