The mixture makes things harder to troubleshoot, but assuming everything more/less fit before and you haven't done anything odd like put non-vented rotors into a caliper that is sized for vented rotors (from the pic it they look vented), you should be able to return the system to good order.

Did you replace the gaskets from the booster to the MC when you swapped it out? It's possible you have an air/vacuum leak there.

Or, since the problem showed up when you replaced the MC, you might a) have a bad MC; or b) have trashed the seals in the new MC by using full pedal travel in the two-man bleeding process.

I'd focus on troubleshooting the MC or outright replacing it to restore proper feel and safety.

This assumes the basics in the bleeding process were done, like never letting the reservoir get empty while bleeding. Three quarts is a LOT of fluid to push though. Maybe pints, in the small bottle?

"Bedding in" or "seating" pads may mean slightly different things to different people. My understanding is you're getting the piston/pad/rotor relationship correct after you've installed a new pad/rotor since the distances have changed. "Bedding in" takes up the slack in the system caused by depressing the piston in order to make room for the new thicker pad or rotor. It may also refer to wearing away the edges of the pads or rotors if they weren't a perfect fit and you didn't have them turned; for example the outside edge of the new pad might just touch a small ridge on the old rotor. The slight difference may require more pedal travel to create stopping force until the ridge wears away or a groove is formed on the pad. If you've had the problem for two years, I don't think this would be your problem.