First thing to do is make sure you have the cockpit between the "A" & "B" pillars well braced, and only do one side at a time.
When I replaced the floors, I drilled all of the spot welds I could get to, but some cutting with whiz wheels, body saws, chisels and grinders were neccessary. I just used split point cobalt stub drills. The split points stay centered when you start them, and the short stub drills don't bend so easily. I tried the "spot weld" drills, but had better luck with the cobalt stubs.