Hy Gray_Ghost,
1. you say the non running engine is already using the longer water pump that came with the later engines and that everything was in place with no interference problems, so just use the stock pump for the latest transplant engine, it sounds like someone before you has "adjusted" things to make the longer water pump work.
2.drilling the existing mounting plate to match the pattern on the older ones would probably be easier than installing a drilled one. If you drained the coolant and oil you could turn the engine on its side on the stand and drill the plate from the side.
3. the fuel gauge sender does not care which voltage is used with it, it is merely a variable resistor.
4. you may reuse the throwout bearing if it is not too loose and noisy. You will have to install a new pilot bushing in the end of the crankshaft if it came with an automatic previously, I think all the crankshafts were drilled for a bushing, you better check before you get too far.
Hope that helps.
