James,
Yes, these can be a bit of a problem to get to fit. It looks like your problem is that you waited until after the bottom floor was riveted on to do the fit. This looked like it might be a problem to fit later, so I did this while the fuselage was on its back, before the floor was riveted on. It still took awhile to get everything to fit (one side went right on, the other side took a few hours of mucking with). Of course, this doesn't help you now.
What you need to do is to make sure that the hole in the floor and the F-704 flange has clearance all around the weldment where it sticks through the floor. This is a series of "put the weldment on, mark where it hits, take it off, file a little on the hole, put it on, mark, take it off..." One other thing that I did was to use a deburring tool to remove the paint from inside the holes on the weldment where the bolts go through. This helps a little for a few of the bolts that are a little off.
Good luck,
Tracy.