Stator failure?

I am a certified mechanic in Diesel and good automotive mechanic. New to the 2 cycle jet ski engine. Just overhauled a js 550 a6 engine. Gave it a 440 crank, 76 mm pistons, Pro Series connecting rods w/ oversized pin bearings. Got it all back together, was firing. Was setting up to time the stator and when I reassembled the flywheel, I lost spark. Any common mistakes that I could have made or good diagnostic ideas. Any help would be greatly appreciated.