Although I do not have a true solution , I am thinking that the master cylinder is not getting a full stroke with the shortening of the piston rod. Realizing you had to shorten it to install , it seems the problem is there. Not suggesting you did anything wrong but the question is how to accomplish this . First , it would be necessary to determine how much stroke the piston is currently actually moving inside the master cylinder versus how much movement is necessary to properly force fluid out to the lines. Hoping the manufacturer of the replacement master cylinder has this information of the required stroke needed. I'm also thinking that since this setup is not to original design , is the angle that the pedal and piston rod move at different ? If the rod is not moving straight into the piston bore of the master cylinder and some of the movement is lost to the rod moving at sort of an angle due to petal leverage is different , the stroke is short. The angle of the pedal from full rest position at pedal bumper when released to full travel must push the rod straight naturally so maybe it is possible that a new mounting point must be used for the piston rod on the brake pedal . I am just surmizing as I am trying to imagine the before and after of this project. I'm certain it worked before , but we both want to know just what changed and caused this problem. If at all possible , if the pedal and rod can be removed to allow you access the the rear of the master cylinder so that you may attempt to push the master cylinder piston manually to try to achieve so kind of pressure out of the lines. I'm certain you bled the master properly so pushing the piston should achieve some results. If we can just get pressure to get fluid into the lines just to prove that portion of the project is successful , which I'm sure it will , that will show that the pedal angle and leverage point needs to either be readjusted or reconfigured altogether since the leverage angle may be wrong and not producing a straight stroke thereby losing piston movement in the distance the piston is required to travel. I'm also hoping the manufacturer may have a viable solution to your application . Hopefully not have to lead to a purchase .
With that said , anytime that piston rod distance is changed , even minutely , it effects master cylinder piston travel and affects braking , especially with a power booster. I would say your first plan of attack will be to try to manually push master cylinder piston manually as previously described. Am hoping for the best at producing pressure so all that is left is redesign of the pedal movement if necessary and if piston rod length may need to be tweaked . The rod length is an important factor and am not sure how to further advise you exactly what length it should be .
Hoping another member that has had this experience may be able to assist you as well .
Best of luck on your project and I believe your still close to the finish line . Greg
