Those holes should already be drilled and tapped for the tranny side bracket and studs. With out knowing what you pulled the bolts from, showing us pictures with them next to a tape measure isn't gonna help us identify them.
I don't know what that first picture is but it's not for a 6th gen.
The holes are just holes as far s I can tell. I'll double check when I get home on Saturday. But when I was working on cleaning it I put a screw driver in to feel for threads and felt nothing.
All of those parts are from a 93 accord LX. The two long bolts I believe are for the starter and tranny, but I dunno which one for which, that's why the tape measure is next to those... Hopefully someone will remember which one is longer. Other parts the bolts could have come from are the shifter cables, fluid resovoir, or clutch master cylinder.
Hope that clears some stuff up!