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Assuming all the air is truly out of the system you may have a bad master cylinder. It's not unheard of on older vehicles for them to have a soft or low pedal after a hydraulic failure. The pedal traveling so much further than normal during the loss of pressure and then the bleeding can damage master cylinder seals that had been otherwise ok.
The proportioning valve could potentially cause issues but in a case like this if the proportioning valve was causing the problem I wouldn't expect normal flow if at all to the rear. The valve will sometimes get stuck after a fluid loss like this.
Try pinching off each rear brake hose one at a time and see if the pedal gets firmer. If so then you still have air trapped in that respective caliper.
If that doesn't make a difference then you can remove and plug the lines at the proportioning valve and recheck the pedal, and you can also plug the lines right at the master cylinder for testing if needed.