If the rod was too long wouldn't that just block the compensation ports when brakes were off keeping residual pressure on and start to drag brakes because piston did not return fully?

Can you post a picture of your combination valve? If a late model that combination valve has metering and proportion all ready. You state you have a proportion valve in rear with brake light warning? What about the combination valve warning?

I think you just need a distribution block as mentioned. That just distributes flow and it will have warning light for failure of one side. Then with your adjustable proportion valve you can set your balance.

A Mopar MC has the primary piston for the front brakes at the rear of MC (large reservoir). The smaller secondary piston is at the front of the MC. If you open the front brake bleed valves and press brake petal the front piston can collapse to the rear piston and full travel. When you go to bleed rear, and the pedal stops that is because the front piston seems to lockup before it collapses enough to move the rear piston sufficiently.

So either you have issues with the combination valve or some other problem preventing sufficient pressure build up at either set to even lockup a wheel in gravel. Pressure gauge can help you determine where the issue is. But your statement car never had good brakes and you still have your combination valve original, would lead me to get rid of it, and get the plain distribution block in.

You can gravity bleed and I use a small inexpensive vacuum pump kit to bleed brakes.