Braking it down...

Do you own a Mity-Vac handheld vacuum pump? They go for around $50 and it's a worthwhile diagnostic tool to have around anyway. By attaching to the wheel cylinder bleeder, it will allow you to draw brake fluid all the way from the master cylinder. If your MC is good, (and it was before you painted your engine compartment), and it's properly bench bled, and the shuttle valve is centered, and none of the brake plumbing is crushed, you will get fluid to your rear wheel cylinders. Keeping bleeding it with a helper...down > open >close >up, or get a pressure bleeder or mityvac.

Do you get brake fluid under pressure if you crack open the rear brake line fitting at the master cyl? If it's bench bled, then you should see a good sharp stream of fluid if you crack that fitting with the pedal pressed. Is the pedal going to the floor with all the fittings tight? You should have a partial pedal if the front brakes are good. Also, if there is no fluid in the lines at all, and you press the pedal hard enough, that pin could shift back on you. You can open the fittings on the distribution block and trace through the plumbing until you lose the pressure.
THe first part is important, cause if the master cyl went back on the firewall and has the plunger even slightly depressed/pushed in, you will lose most of the back brake bias. Make sure nothing hung up when you put the master cyl back on. THe pedal rod should be just barely short of touching the back of the master cyl piston. All the bleeding in the world will not solve that. Make sure you are getting fluid under pressure at each point in the system. It's tedious. We just finished up a 68 Galaxie with this exact problem. Had the wrong booster to compound the problem even worse. The owner had also removed the spacer plate from behind the booster.
Does this car have a power booster?

And the brakes worked fine right after the booster was replaced?
Assuming the shuttle pin has NOT slipped out of center, can you unbolt the master cylinder and leave the lines attached. Make sure that the master cylinder piston is not being depressed at all when it's bolted up tight. THere should be as little clearence as possible, but clearence none the less. THe push rod should be just short of touching the master cylinder piston. Is it called a ram? It's hydraulic...

I don't think there is a spacer on the 67-68. I looked over www.partsamerica.com. THere are a couple different Bendix styles.

Lets go back. You said you cleared the rear brake lines of all fluid. How did you do this? If you blew air in the line with the lines off at the rear wheel cylinders, where did you inject the air? If you did this right at the line off the master cyl, did you get air out the other end?
Let us know about the clearence on the pushrop. Also, if it is adjustable. It should be with a new power booster...
On the Galaxie, the adjustment was all the way down-as short as it would go, but it was still depressing the master cyl about a quarter inch. THis was enough to lose all the rear brake bias. When we spaced the master cyl out with some flat washers, we had brake fluid flying out the back lines. About that time the owner showed up with the spacer-he thought we might need it...that's probably not your problem, but I'm not sure what else to check first.
You need to get it to the point where you can get pressurized brake fluid squirting out the rear brake line fitting at the master cylinder with the brake pedal held down. THen you can move on down the line and solve the rest. Sorry, it's so much faster to do it than to write it.