Hi Roel,
I started to think it would be a snapped conrod but the engine still ran rough after you freed the clunk. So, can't be the conrod coz once the conrod breaks, there is no enough compression to start the engine and to push the piston up but the engine still starts. You feel a clunk when you spin the flywheel grill manually but you freed the clunk when you spin from the underneath because it has more torque/force. One thing I can think of related to tilting the engine is a foreign object that slide and stucked into the flywheel magnet between the grills which product a clunk when you rotated it 360 degree. Possibly forcing to free the clunk also could knock off the ignition coil which possibly the engine won't start. Worth checking the ignition coil.
Cheers,
CM
