A theory?
The two Mekugi-ana got me too. If it were a post war bodge, that would not explain the two holes; sure, you could say "parts replacement saya, tsuka, etc." but for a machine made blade? So, the second hole was made for this tsuka. So what could have come before it and explain also the tsuba? Sherlock says "A for military katana, converted to a gunto, tsuba retained". We all don't want our own bodges / parts swords, I know. But I did not pay a fortune for it and really it is a case of do I keep the tsuba as part of its war time history, or buy a regulation gunto tsuba and replace it? The thing besides the two Mekugi-ana aspect for me is that the tsuba (brown) sort of matches the saya colour wise; is that because the tsuba has since patinated (tend not to think so)? And yes, Bruce, you are right, a lot of saya paint has worn / come off.
Keep the tsuba as part of its WW2 history?
Or buy a gunto tsuba and sell the copper one?
What would you do?