If you are working off any edges besides the repaired area, STOP IMMEDIATELY!!!!
You may have already filed off too much at the repaired area. It may need to be built back up again, then the repaired area brought back in line with the rest of the undisturbed body. If you start removing material unevenly, or on the non-repaired sections, you risk having a too-tight gearbox that will either not work, or possibly fail.
author "Old Bikes"
too many bikes to list, including:
JPN, 952 Prototype, MkIII Interstate, Combat Dunstall, VR880 SS, Triton