If the head and or bed were twisted and the machine ran itself in that way, if you reassmbled it w/o the twist/bend/whatever, you may have gotten the axis of rotation askew.
The think may want to be tightened down in a certain sequence or to a certain special torque - over or uneven torquing might cause sticking and binding.
Sometimes, old sleeve bearing stuff should not be disturbed for these very reasons. You're gonna have to take your time and do some experimenting to nudge caps this way or that and try to find the sweet spots where things will be properly tightened and yet the thing will still turn.
That or else line bore the housing straight/square and grind the spindle journals to the proper fit/clearance as well.
Time and patience, time and patience, with the situation you're in....