I would certainly recommend another off the car bench bleed of the master. With what I read it sounds like there are air pockets in the master. Here is a link to our truble shooting guide as well:
http://www.classicperform.com/Instru...brakeguide.pdf

Being that the proportional valve has a internal residual; the use of a vacuum bleeder like you are using will not work as well as you would think. Nothing is going to beat/compare to a traditional proper bench bleed and old fashion pedal bleed.

In the article above we also explain a Syringe method of bleeding the masters that also works well.