Large bolt pattern brake HELP! HELP! HELP!

What size is the master cylinder?

There are two as I'm sure you know, 15/16" and 1 1/32". Doesn't sound like much, but it can make a big difference. And that's not just a manual/power size issue, each type is available in both sizes. I believe it was a 9" drums vs 10" drums/disks thing. Either way, you can't count on most parts guys to get you the right one.

The calipers being switched side to side shouldn't cause any issues if the spindles are swapped side to side to move the position of the calipers, they bleeder will still be up.

Are you seeing any leaks anywhere? The condition you describe of the pedal hanging up for a second and then going to the floor sounds like a leak. If its not actually leaking fluid out of the system, it could be the master cylinder is losing pressure past the seals.