The parts book isn't any help. It just says mounting hardware items are standard stock. It looks like the two smallest holes at about 11:00 and 5:00 positions are pilot holes for alignment studs in the timing chain cover. See attached photos of the pump and exploded parts view.
The fan blade, spacer, and pulley will have be removed to get at the mounting holes. Attached is a shop manual page giving steps for pump removal.
If some of the other holes are empty, the depth can be determined by probing with a small drill bit or screwdriver. This will give an idea of the maximum bolt length needed. Then sample bolts can be hand-threaded to determine correct thread pitch and length without bottoming out.
I would say remove another bolt and try it in the open holes, but that's not a good idea. The bolt may snap off due to corrosion. There could be broken-off stubs in the suspect holes. That would require pump removal to replace the broken bolts.
What has been, can be again. (Bob Wills, 1942)