what line go's where?

I think I would get new rear wheel cylinders. The groove in the 'pusher rod' coming out of the bore is where the rubber boot should set, so the boots look to have been installed wrong for a long time, probably not sealing right, and likely there is rust inside the bores.

And yes, after reading this thread a coupla times, I suspect a lot of air in the MC. I'd take it off the car and bench bleed again. IMHO, don't use the simple output port plugs; use steel or rubber lines on the output ports that loop back into the reservoirs. These do a much better and faster job than the solid port plugs found in some kits. Make sure the MC is level when you bench bleed it, and don't have the pushrod end tilted up.