Hmm, sounds like someone filled them in at some point maybe.
If you look on the engine compartment side of that area, is there a vertical brace (looks like a u-channel welded to the firewall) in about the spot you think your pedal might go?
If so, that was where the holes used to be. It's an additional brace for that high-stress area when you're really cranking on the pedal.
Got pics of your floor and pedal so we can see what you're working with?
There are also pics hereabouts, but I haven't saved any handy links for you to check out. I'll do it if I come across some, but do some digging too, if you haven't already.
Seems to me I saw some pics of the area just recently in fact.
Hmm again. PM thegreatjustino here. For some reason I remember him posting up. Maybe it was one of his pics? Don't know, but might be worth a call. Tell him I was bandying his name about maliciously, so he won't get too upset and being disturbed! ;D
Just kidding. He's got some good pics of a lot of different things. Maybe he can help.
I've only got pics of the brake mechanism and some of the cable routing underneath.
Good luck.
Paul