I ran one new line to the junction block area and just replaced the junction block with a coupler for the front brake. I ran a new steel line and hooked to the rear brake line using another coupler. Ended up just replacing the front junction block with couplers for each line. I plan on keeping the original junction blocks since they are expensive to replace.

Interesting thought about the plunger rod. I am using the rods supplied with the conversion adapter kit, but it is the same length as the OEM rod with the single chamber MC. Not getting much flow no matter where the pedal cycle falls. In fact, there was not much flow when I was bench bleeding the unit. Ordered a MC for a 3/4 ton truck that should bolt right up and will pick it up Sunday. The local Autozone has been really good about the problems and said they would take the defective one back with no problems. Never had issues with reman products before, so wondering what else is going on. Have double checked all lines for kinks or restrictions, but all are good. Used a tubing bender to keep my bends smooth.

I did some searches for info on dual chamber master cylinders, but will go back and try again using brake problems in the search function.

Thanks for the suggestions! Will let you know when I resolve the problem.