Hello,
I had the exact problem with the stops on the halyard hanging up on the end of the sail track when lowering the main. I decided that to cure the problem, I would want the keep the halyard on the outside of the track (since it hooks to the sail, which is on the outside) This was easily accomplished by installing a round head stainless stell screw at the top of the track. (I think it was a #10 x 1") It's just below the pully in the back of the track groove. Experiment with how far you turn the screw in, since it stands out about 3/8". Since it has a round head, the stops don't hang on it and it doesn't cause any friction when raising or lowering the main. After I installed the screw, it cured the problem 100%.
Jack