Just grind it, you will be bummed when you have a hole in the bottom of your new pipe. You want the chamber and the headpipe opening to be parallel to each other, that will determine where the end of your pipe sits, shimming your waterbox up and pushing the pipe out of alignment could cause premature coupler failure. Take a couple pieces of turf (or some sort of foam) and wedge them into the front waterbox strap hooks (with the straps installed) this will keep the straps from falling off the hooks, then when you go to install the pipe you can undo the front of the straps and move your waterbox around as needed to get the chamber in there (makes things a little easier). I sometimes remove the battery box too, it makes getting the gas tank in a little easier. Some WD40 or really anything slippery sprayed on the exhaust hose will also make getting the gas tank in easier as you have to kind of shoe-horn it in there once the chamber is installed.