So from your description, and the diagram in the link you provided, bolt #4 should have "a liberal amount of RTV on the end to seal the bolt threads". I guess after installing and allowing the RTV to cure it is resistant to the coolant.
The PO did extensive work on the car recently, including the engine / tranny swap. Now I'm wondering if the leak could be the a failure to apply the RTV??? Once I get some stuff moved out of the way I might be able to get a better idea of where the leak is coming from. My guess is that a water pump would typically leak from the shaft seal?
I have always understood that the two engine bocks are nearly identical but when I look up the water pump part number for both the stock 86 Fiero 2.8 and the 94 Camaro with the 3.4 they have different part numbers and the price for the Camaro pump is significantly higher.
The 2.8, 3.1 and 3.4 blocks are essentially the same with bolt on parts being able to be swapped between them. The 3.4 water pump rotates opposite the 2.8 because it has an additional pulley in the system. It will not correctly bolt to the 2.8 timing gear cover and flow the coolant in the right direction. 
I forgot to mention that if you are replacing the pump or loosening bolts on the pump, you should first install the timing gear cover clamp so that the timing cover doesn't separate from the block and cause coolant to leak into the crankcase. Some replacement water pumps come with the clamp, others don't. 
