78buckshot, thanks I suspect that you are correct about the problems being related at least in part to the short vs. long water pump but I beleive the short pump provides 1 3/8" more clearance at the front of the engine for fans/radiator.
Jerry, thanks for the input, there is material to drill holes for the alternative bolt pattern in the pulley if I keep the pulley and if the clutch/fan is going to be used. I don't need to drill the alternative bolt holes if the clutch/fan will not be used. I had not thought about shimming out the crankshaft pulley to align with the water pump pulley so thanks for that suggestion.