When you're putting it back together, just match the threads and carefully screw the longer ones in place. If they bottom before the head hits, then use a shorter one.
If you have any left over, just toss them in a old coffee can, the traditional container for leftover bolts.
Hard to tell from your pics on size, but those may be for the rear engine mount. The shorter ones may screw into threaded holes in the bell housing to hold the mount in place, and the longer one down thru the mount bracket and the crossmember with lockwasher and nut on the bottom. That's a WAG for sure.
