This may be something to check. When I did a vr6 conversion on my mk2 I initially used the 280mm setup with a second hand corrado brake master cylinder. When I drove the car for the 1st time the n/s/f wheel was locking up and the pedal feel stiffened. I ended up removing the brake hoses going to that wheel, checking them and ended up replacing the Rado brake master with a new G60 brake master which completely solved the problem. The Rado master had some form of blockage, due from rubber breaking down/being old so maybe you have a similar problem. Also brake hoses can collapse/deteriorate internally and a small flap of rubber inside can prevent fluid travelling one way or another causing a stiffer pedal or uneaven braking after you have presuurised the system from braking a few times.
Either trial and error fitting new parts or you could take it to a garage to see if the wheels are braking evenly, if not then it could be a hose/hoses, if they all brake evenly then it could be the brake master. Sounds like you have checked the servo for vacuum leaks as this has been mentioned previously.
Hope you get it fixed
