If you ever ran the reservoir dry, during your brake swap or brake bleeding, maybe you need to bleed the master cylinder. Even when I have ran it dry, I have never had to bleed it, but I hear some people do.
In what order are you bleeding the brakes....which wheel do you do first, second, third, and last?
Have you tried bleeding the proportioning valve? Again, I have never had to, to fully bleed the brakes, but some people do.