I'm not sure what the problem is but if it was me I would put #1 piston at TDC then using some sort of spring compressor to actuate the valves to check for interference with the piston... then do repeat on the other cylinders.
(I've never had one of these engines apart but it sounds to me like you might be hearing a piston hitting a valve)
I hope this helps, make sure you get back to us after you get it fixed, good luck.