The noises you described when the engine was struggling sound familiar, I've got 'em when the fuel pressure in the rails was too low. In my case it was due to running out of gas (duh). In your case, maybe one of the fuel fittings came loose from your reinstall (BTDT). Is your fuel filter or pump in the back by any chance? Was the "clunk" possibly one of these things dropping on the engine tin, or was it a more authoritative clunk? Busted engines usually don't p*** gas all over the place unless something severed a fuel line, but you woulda probably seen that go by on its way out of the engine well...
Good luck!