Try correcting the nock low with the shortened shaft and see if that doesn't correct both problems. I have found that I need to change my nock height while working on trimming a shaft to proper dynamic spine. Take a good measurement of brace height and nock height where it's at now, and write it down so you can go back to exactly where you're at if you don't like the changes you make. As far as that goes, you can raise or lower your brace height to simulate a change in center shot. Lowering your brace will yield similar results to building out your side plate, and raising it will simulate a closer to center shot. If you lower your brace, and arrow flight cleans up, then your current shaft set up is too weak for your preferred brace height. Likewise, if you raise your brace height and arrow flight cleans up, your current shaft is too stiff for your original brace height. Adjust strike plate thickness accordingly.