Thanks Brandon. I don't actualyl have an intake manifold bolt stock in the engine block. Thank goodness. My problem is that I can't screw the bolt back into the hole because the strips in the hole must be bent. As evidence the first two strips of every bolt that I try to screw into the hole gets bent and warped. This gives me hope that the problem is way up at the beginning of the hole. If re-threading with a tap doesn't work, then I'll just drill only a tiny amount to cover at least 2-3 threads of the whole to remove the damaged threads there.

As for those yellow plugs that I mentioned above, I looked at the area where I found them and I believe that these yellow plugs are just to cover the hex screws along the side of the engine block.

Thanks.