Trying to figure out brake problem with rear disc upgrade

[Hydratech®]

If all else fails, you may have to get into port plug diagnostics. Even though this article is written for hydroboost applications, the basics still apply to a manual or vac assist brake package: http://hydratechbraking.com/Hydratech/braketech1.html

For instance, you could plug the ports at the rear axle flex hose, obtain a good pedal, THEN connect one rear caliper at a time, bleed it out and see what you've got. Since this axle was handled / transported, it strikes me that you may even be fighting an ever so slightly tweaked caliper mount bracket (that could've been thumped while wrestling the axle around).