The four very long bolts/studs go all the way through the water pump, timing cover and thread into the block. The shorter ones thread into the timing cover. To double check, hold the parts in place, and place the screw in its hole, without screwing it in. There should be about a half inch space now between the fastener and pump body, indicating that there will be about a half inch of thread engagement.
You didn't say whether you have a 302 or 351. On my 1994 351, this is the location of the four long capscrews / studs:
Upper right- stud with 5/16" threads sticking out.
Lower right- Plain capscrew.
Upper left- stud with 5/16" plain rod sticking out.
Lower left- stud with 3/8" threads sticking out.
Right is right side of vehicle with parts installed.
N.B.: On my engine, these studs aren't used.
I would not use silicone on the gaskets except for possibly the end seals of the intake manifold, and even there, sparingly. The intake manifold gasket should already have silicone bead printed on around the ports. The one piece oil pan gasket does not need any sealer, the older three piece type can use some "black goo" type sealer. Silicone is risky because excess tends to squeeze out as drops inside the engine, which cure and can get through the oil pump pickup screen, clogging the oil pump pressure relief valve or an oil passage with disastrous results.
