Not sound like a smart A**, but are the front and rear lines of the master cylinder on the right ports? I plumbed one backwards, and it makes the brakes act really weird. If it was one side I would suspect rubber brake line, but both have to be master cylinder. Back off the master cylinder rod just a bit more and see if the problem goes away. Be sure the return spring holds the lever weight off the rod. You could end up with to much free travel, but it will help diagnose the problem.
