I think you are probably right - if you get the clunk even when gripping and turning the axle input flange then it does sound like somethink actually in the axle.
But the test you did at the wheel bearing - you mean you can pull the shaft in and out axially? That certinly means wheel bearing wear, but as you say that may be all.
I would get another scrap axle, but to start with just swap over the hub and shaft assemblies. That is very easy, with no major dismantling, and that would then help you locate the problem. It might be cured, or if the clunk remained then you could go on and swap the whole axle.