OK guys, let me clarify. I did test each mod in succession instead of blindly adding them one after another. As a former GWX and WAC player I'm used to checking each mod in turn.
However, the periscope lowering problem is/was present even with only the NYGM mods (the first 3 in the list). I added further mods in the hope it may stop. Obviously not.
@h.sie - As already mentioned above, the periscope problem was there
before I patched my SH3.exe file which I believe you are referring to, so no reason to be so astonished.
Having said that I have since done a fresh install and, as before, I still have the scopes lowering when I don't want them to. Stock SH3 is fine, but as soon as I add NYGM it occurs.
EDIT: Regarding the overwrite messages - these refer to adding the mods in the order described in this list: http://www.subsim.com/mods1/nygm/ I assumed each previous version of NYGM can be safely overwritten, hence my original comment.
I can't see how there are any orphan files left over from a previous (and distant) GWX install...
This weekend I can spend more time on it and I'll do a complete re-install, again with further testing.