Sounds like you have an air-loc.
I used this to bleed the brakes. It might be the answer. Its better than pumping, opening and closing bleed nipples.

NEW GUNSONS EEZI-BLEED BRAKE AND CLUTCH BLEEDER KIT | eBay

 

When I had my proportioning valve replaced, I had to bring it back to the shop after a month or so because the problem recurred. They re-did the job (under warranty) and it's been fine ever since (five years).
I think what happened was that flushing the system loosened up a lot of gunk and it clogged up the new valve all over again.
Try taking the proportioning valve out again and cleaning it out as well as you can. Also do the same with the master cylinder. Then flush the lines before you close the system back up. Start by flushing the lines to the proportioning valve, then the lines to the wheels, then the calipers and wheel cylinders.

 

I went to the local dealer today and spoke with a guy there about it. He says that the proportion valve being clogged up could have caused the master cylinder to blow out its o-ring because of the amount of high pressure the clog would generate. He said if I were to take it to them they would replace the master cylinder and bleed the system then go from there. So it looks like I'm replacing the master cylinder again tonight and flushing the system some more. I did dismantle the old proportioning valve and found a lot of buildup in the spool so maybe the dealer is right in his assumption. Hoping for better luck tonight that's for sure!

 

So here is what I learned throughout this long, dreadful process; the proportioning valve clogged causing no fluid to the rear drums. I blew out the lines and replaced the wheel cylinders for fear of contamination. Bled the system and had a new completely different problem. I got to thinking about the clogged rear lines and thought maybe that pressure exceeded the master cylinders capability. When I removed the m/c I found both of my problems. First problem was the massive amount of sludge in the rear of the reservior. Second and equally as important was what I found when I pulled the m/c from the booster. The end of the pushrod on the m/c had a plastic tip that mates with the booster actuating rod. For some reason the tip broke off and fell about and inch out of alignment. This caused my problem when the pedal was slowly applied. I can only assume that when jamming the brake pedal momentum bounced the tip in place enough for the car to stop properly. I replaced the m/c and cleaned the reservior thoroughly. It got dark so I will pressure bleed the car tomorrow after work and with any luck I should be back on the highway! In all my years of repairing vehicles I have never seen such a difficult brake system to repair! Will update after the system is bled. Thanks to everyone for your input and assistance!!!

 

It all sounds good except the part about the pressure exceeding the capacity of the master cylinder. The pressure in the system is all generated in the master cylinder and it only comes from your foot on the pedal assisted by the brake booster. No matter how much gunk there is in the system it won't increase that pressure. The whole idea of an hydraulic system is that the pressure is equal throughout, so the bit about excess pressure on the O-rings is just hokum. Anyway, now that the system is clean let's hope it works properly.

 

I can agree with that as it makes more sense to me. Bled the system tonight and.......best brakes it's ever had!! Better than new!! I think the broken tip on the m/c happened this week but the clogged valve was there when we bought the car. Boy have I learned a hard lesson on the value of flushing the brake system. I pray to never fight this again on any vehicle lol. Thanks to all for the help.

 

With all the parts you replaced, the system IS new. Glad to hear it is back working again. Your post about the guy at the dealership reminded me that when I was experiencing the problem on my convertible, I brought the car to the dealership. I had no braking action on the rear wheels. That was obvious because the rear discs were all rusty. The diagnosis at the dealership was a contaminated system, but the remedy they proposed was to rebuild the master cylinder and all four brake calipers and flush the system. They quoted me $1400 for that work. The guy insisted that half of the master cylinder was clogged up. I knew that couldn't be the case because the master cylinder is split between diagonal wheels, not front to rear. The guy then insisted he was a certified brake mechanic and that I was just wrong about that. I took the car elsewhere and never went back to that dealership, which has since closed. The concentration of the problem at the rear wheel caused me to suspect the proportioning valve, which sends a little less pressure to the rear wheels. I discussed the problem with the second shop and that (eventually) got the problem fixed for about $300. If I had let the guy at the dealership do it, I would have been out an additional $1100 and it wouldn't have fixed the problem at all.