You can run the Cabby 5-speed, but it will have a 9A trans. That means 3.67 R&P, and a .89 5th gear. It will be OK, but not great. You won't have low-end torque, and you may have high RPMs on the highway. You'd be better off getting a 5-speed transmission that it better suited to the diesel. But if you're putting on a turbo, that will help. You may want to keep the 9A trans, and swap in a .80 5th gear. Who knows. But, you'll want to do some research on gear ratios. If it were me, I'd try the cabby trans for a while until I figured out what i wanted for power/MPG.
You can use the clutch and flywheel from either, but you'll need to compare the TDC marks between the gasser and diesel flywheel to make sure they're the same. They should be (TDC= the notch with 'O' beneath it). The gasser will have extra marks that do NOT mark TDC. They're used for ignition timing.
No worries on the flanges. You can just swap the inner CV joints. I'd suggest you swap the flanges, but the 4-speed flanges won't work on a later (1983-up) 020 transmission with limited slip. You'd have to find 90MM flanges from a 1983-up trans.