Hi POLQWA, You are correct the crankshft & rod is one assembly [piston is separate item]. I have never seen a crankshaft go bad on the new edition Whizzers. I have even rebuilt motors that were run completly out of oil, and the crankshaft was fine. The only issues I have ever run across concerning the crankshaft was one that had "twisted" [do not use a power driven impact wrench when tighteneing the flywheel bolt], and the motors that had run out of oil needed the bushing at the top of the rod re-surfaced [where the wrist pin attaches].
Another area that could be causing the problem could be the sparkplug, and or the valves hitting the inside of the head. I haven't run across the sparkplug problem, but I heard some of the earlier NE heads were made slightly different, but usually hit the sparkplug and closed the gap [wouldn't start].
If you have the copper head gasket [re-usable], I would suggest you remove the head and look at the combustion chamber to make sure nothing is hitting. I once worked on a motor that the wrist pin clips weren't installed on one side, but it didn't make a "thumping sound", just started to smoke [ruined the cylinder wall]. You might also check the piston for possible cracks [never had this happen] and take a good look at the wrist pin for extreme wear. You might also take a look at the alternator coils under the flywheel to make sure the bolts holding it in place haven't loosened and allow the flywheel to contact the coils at higher RPMs. I am sorry I can't be of more help, but just never had any similar problems with the Whizzer motor..............
Have fun,
Quenton