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While rebuilding my 79 L-48 to a 383, I replaced the stock timing gear cover with a polished aluminum one. Now I find that the stock short water pump will not clear the new cover. Will a long water pump fit and clear the cover? Will this change the position of the fan or will it remain the same?
Yes, a long water pump will clear the Timing Cover.
Yes, a long water pump will change the position of the fan, and belt alignment for Alternator, Crank Pulley, AC, Power steering. Summary, to get a long water pump to work, you will have to do a lot of work to get everything to align.
I haven't done this, but I think many have had success with using the Cloyes Aluminum Cover, with a small amount of grinding on one or more bolts on the back of the watter pump.
-Jim