Square pegs never fully fit inside round holes perfectly. Best case scenario are "gaps" in functionality. If I were in your position, I would keep the guitar as is and adapt or simply sell it and get something that works for you. I have tried for years off and on to "learn" to work with a middle pickup in a guitar to no avail. I have sold some amazing guitars that I probably should have just yanked out the middle pickup and kept. I can understand if the guitar is really meaningful to you or you are attached to it to want to keep it and no worries there. If that IS the case, leave it alone and keep it. If that is not the case I would sell it and get something aligned and better suited to your playing needs. Good Luck!