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There's a raised, round section with 3 dimples in it that gets a couple inch diameter hole drilled it in for the linkage to come through. That's the only hole in the floor. Here's a picture on my car. There's a rubber boot that gets screwed into the floor, the screws go into each of those 3 dimples. The orange circle should show roughly the size of the hole, I'd get the boot first to make sure I didn't cut the hole bigger than it needed to be, but as long as you leave some room around the 3 outer dimples you should be fine.

Ignore the sharpie marks on the floor, those are for a 4 speed...