Glad you found the problem! Take the rod out and inspect. If I recall correctly there is only one end that you want to grind, the other is tapered or something. you want to work on one end only anyway to help keep square. My master cylinder and booster were ordered together but didn't have any instructions about modifying that rod. Seems like they should figure the correct length ahead of time. Mine did have two rods but they were very different in length, obviously for a different application. In any case, now you can fix it and enjoy your new brakes.
I used an angle grinder with a thin disc, held the rod perpendicularly and rotated it while grinding. Just go slow a make sure you have something to measure it with like dial calipars. Take a little at a time and sneak up on it, obviously if you take too much you can't put it back. After you've got it shortened just barely chamfer the edge to remove any burrs. Good luck!