One thing to check would be the timing belt tensioner. Others here have had a tapping sound when the engine was running and thought that it was something IN the engine only to find out that the timing belt tensioner was bad and was allowing the tensioner pulley to "flop" around causing the tapping. That could also throw your timing off a bit as the belt isn't as tight as it should be.
It's a fairly cheap and easy fix, but you do have to get a lot of stuff out of the way in order to get to the timing belt tensioner.
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