In most motorcycle engines, the piston and valves will hit each other if the timing is far enough off.
If you heard any noises like this, you should remove the head again and check for bent valves as they have a habit of breaking off the head and eating the engine.
If the valves did hit the piston, they will have left a mark in the piston crown.
Wait until you get a copy of the valve timing instructions for your bike and follow them religiously. A one tooth error is enough to screw it up royally.