2004 FX140 ignition timing off

Hello! I was given a 2004 Yamaha fx140 from a family member. It started fine but had a significant rod knock. I have lots of experience with older two stroke skis but this is my first 4 stroke. Pulling the motor was no problem, found the bad bearing, replaced it and the rod, cleaned the whole oil system out. After getting the motor back in, the ski won’t start. Turns over fine, I have fuel pressure at the rail. I have spark but I believe my ignition timing is off. I found top dead center of the rear most cylinder and put a marked line on the drive coupling. When I used my timing light it wasn’t flashing when the mark was at the top. I didn’t take off the fly wheel but I did spine the gear on the crank because it spins freely one way. Would this or anything else I’m not aware of mess up the ignition timing? Any help is greatly appreciated. Thank you!