Retarded/Advanced/Stock Timing Settings

Today I pulled the flywheel off my bike to check the timing. It knocks and backfires under decelleration so I thought it might be detonation because of advanced timing? I've got one question. I think timing was off from the factory, but am not sure where the marks should line up. Should the mark on the plate line up with the middle timing mark? Mine was slightly to the right, so I adjusted the plate until it lined up up with the middle mark. It was slightly advanced, right? I started the bike, and it wasn't any better. It makes terrible racket when cold, so I warmed it up, rode it down the street a few times, and it got better, but no better than it was before when warmed up with advanced timing. Should I retard the timing even more? I'm jetted stock right now, and would like to get this problem nipped. Any advice?

gooby, It's in the middle now, and don't worry, my dad knows what he's doing, we just didn't know the stock setting. Mac, I run 93 octane, wich is probably fine for a stock 200. What octane do you run now in you're 225? What did you run when it was a 200? I don't think it's jetting. Symptoms lead me to believe it's a lean condition, but I'm already richer than most guys.

I've never heard of a crank bearing going bad unless you are sucking air and dirt, but I'm pretty sure I'm not. Mac, when running you're 200, did you notice the pinging I described, 1-2 under decelleration, and when you blip the throttle slightly when in neutral, pings/knocks on it's way back down to idle? Mine makes all kinds of knocking/pingin/ noises when cold, and you hold it at 1/4 throttle, but when warmed up and cleaned out, none there, only when reving, or under decelleration. How could I tell if I'm sucking dirt and air?