certainly the clunk could be stuck in the front of the tank. This you should be able to check out visually, or if this is difficult, try this: fill the tank one third full. start the engine and hold the plane straight nose up at medium speed throttle for 30 seconds or so.

It is unlikely that you are having problems due to down-line travel. we all fly downlines and we are never nose-down long enough to kill the engine. The lines inside the tank could have fallen off the stopper or the clunk could have fallen off the fuel line inside the tank. I'd look for plumbing problems like this before tearing into the engine itself.