2000 Griz 600 pulsar coil trouble

Hey guys, new here. Got my griz new in 2000 and has been a great bike. Lately it’s been getting harder to start then finally it just STB and wouldn’t start and got no spark. I found out that the pickup coil was wide open (1Mohm) when I measured it. So I ordered a new kit that came with the Stator/pickup coil combined, a rectifier and gasket from Caltric on ebay. I installed per the shop manual and when I put the case back on, the magnet on the pickup coil is interfering with the fly wheel bump out. I manually turned the flywheel and the bump out got hung up on the pickup magnet. I tried and tried to reposition the pickup coil to no avail. The only way I can think of to get the recommended air gap setting for the pickup (.015in or the width of a credit card) is to file down the magnet to get it into spec. Did they send me the wrong kit? Can I gingerly file this magnet down? Or do I send it back and hope they send me a new one in spec. Has anyone ever encountered this problem with aftermarket pickups?