The description of your issue sounds like using the brakes on a power brake car with the engine not running.

You ever (with engine off) popped a PB in neutral and let it roll a bit then hit the brakes. Is that what you are describing?

You running a PB MC W/O a booster?

I would put in a correct MC for your application. I used a 1974 "A" body manual disc brake MC on my '65. Works fine.