I assume you have done all the things consistent with a floor replacement (ie., removing at least the edges of the belly pan and banana wraps, removing the lower most inside skins, etc.). So your approach is a "shell-on" floor replacement. In this case, you want to drill out as few rivets as possible (ie., leave the hold down plates alone, and leave the C-channels attached to the shell). You will likely have to split your plywood sections in half in order to get them to slip under/into the C channels (especially at the ends). This splitting will require you to scap them back together with a "doubler" underneath.
To be honest, though, you are doing a shell-off with the shell still on, which is about the hardest way I can think of to replace the floor. You are about 90% of the way toward doing a shell off, and I would recommend going all the way and just removing the shell. My tool/method of choice for this is a set of home-made gantries and a couple of chain hoists.
For more tips, do a google search for "Airforums shell-on" and you will get several hits from the forums discussing the tips, tricks, and challenges of your operation.