Realize I should clarify that its unlikely the proportioning relates to your pedal feel issue as you've described it. If its working right, it won't start proportioning until something like 500 psi is reached. So when you start to push on the pedal, all four corners will get the same pressure.
The rears help most when you first apply the brakes, so do make sure they are adjusted etc.
One last thought, the brake warning light is also wired to a switch on the hand brake. Its possible there's a wiring or switch issue. The only thing that has me wondering about all of this is that it sounds like the problems started with the installation of the new m/c.
