Recently converted to disc brakes, a 9 inch rear, and decided to swap in new brake lines. Went to bleed the brakes and i can only bleed the front's. I reused the brake line on the axle including the junction box. Could it possibly be clogged with dirt and such?

 

It could be. Try breaking the fitting open where the rubber hose mounts to the body and meets the metal lineat the rear of the car near the diff. See if you get flow from the master there under presure (like when you bleed). If so then the problem is downstream from there. If not check it the same way farther forward on the line where ever you can. Keep moving untill you get fluid flow. Then the problem lies between the spot with flow and the spot without.

FWIW.

Good luck.