small block water pump bolt length?

I haven't seen everything so I'll only state what I know about my own. The lower 2 bolts are the same length as the top center bolt. So the thickness of water pump casting plus 1/2 inch of bolt length should work down there just as it does at top center.
You say you have 2 bolts at 2 inches long, one reaches 1/4 inch or so of threads, other doesn't reach the threads in the timing cover? Has to be a difference in thickness of the water pump casting at these 2 bolt holes... unless something aint right about the threads in the timing cover ( lets hope not ).