Bad knocking under feet

Well.. Its been quite a few months. Much headway has been done to the car. We fixed the starting issue with a new ignition switch. Also fixed most of the wiring, and she idles flawlessly.
However, I think this dart has a curse(joking but not really). It seems once we fix am issue, another very complex issue pops up. I'm aware this is common with old cars, being that I had to replace everything on my engine in my 1970 toyota fj40.

The dart however, is something else. The bad knocking underneath my feet went away, didn't even change anything, but now the car doesn't stall when pressing the brake. All i did was unplug the main vacuum line to the brake booster, then plugged it back in. That fixed that problem somehow, but now another problem has emerged. The rear end has a clunk, and the rear wheels shudder upon takeoff.

From the car not starting when the door is closed, to seemingly magically "fixing issues", to creating another complex problem is very odd. This thing has taken me on a wild goose chase with goofy problems.

And that's where we sit currently

The clunk in the rear end could be u joints, driveshaft, axel bearings, but it seems pretty severe, so I think it’s something really bad in the pumpkin. This weekend I will be able to work on it so we will see what happens.