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You may have to bleed the master cylinder first. Similar to bleeding brakes, except you use a 1-pump method. At the master you will see 2 lines going in. While someone pushes down on the pedal, slightly open the rear line until flow stops, then tighten the line. Repeat this 5 or so times, then head back to the wheel cylinders and keep bleeding. Make sure you are doing the passenger rear FIRST.
Theres air in the lines. Make sure when bleeding the master you have the cap on.
I can assist you further if you like. Your original question was answerd by DriveFast71. Do you need further assistance?
If you do get it to bleed out, I do things differently. The book will tell you to start at the very end of the line first, but keep in mind it is normally assumed you haven't replaced anything, your just bleeding the system. I start at master and work my way down the line following the flow of fluid, from master to combination valve and then to the wheels.
From what you described about bubbles in the master, if the reservoir never went dry when you replaced everything, I would recomend replacing with a new master cylinder, not a rebuilt. At one time I bench bleed 3 rebuilt master cylinders that would not bench bleed out. Finally the 4th one was good. New master is the only way to go. I doubt seriously that your master is any good from what you've told me.
Just like you did when you bench bleed. With pedal down you open the line, and close the line before letting pedal up. Do one line at a time, starting at the first line on the master until there is no air, then go to the next line and do the same thing. Once the master is squirting only fluid with pressure and no air, close the lines and now you should have pressure. Now pump the pedal and hold it down while opeing the line and close it before you let up. Then go to the next place (the other end of that line). Keep doing this action of pump and hold till you get pressure without air out of the out going lines at the combination valve then go to the wheels. You now can follow the book as to which wheel doing one wheel at a time, pump and hold pedal, open bleeder and close before letting up.
If you have ABS, you will bleed at the incomming and out going lines at the ABS modulator. Just follow the flow till there is no air good pressure at each point.. Remember pedal down, open line, and close line or bleeder before letting up.