The added prop. valve is doing exactly what it should be doing back there. That is why the brakes work at all. The trick is adjusting it properly. The purpose of adding a prop. valve when doing a drum to front only disc change is to reduce the pressure to the rear brakes. Drums take far less pressure than discs. The stock combination valve in a drum/drum truck is to distribute the fluid and provide a warning circuit. Now with that removed and a dedicated valve in the rear supply lines the brakes can be adjusted to work, even work well. The problem is you have lost the warning switch capability.
By installing a factory combination (prop) valve it will be set close to what the truck needs as every truck has a different load bias and tire size. Then the rear replacement line set, a front line set specific to discs, hoses and the short M/C to combination valve line will round out the installation. If you choose to install a new M/C (disc specific) then there are even less variables.
Can't advise you on M/C bore size but there tech. line should be helpful.