Its not a grub screw from a cresent spanner possibly? Adjustable spanner ?
Underside of a MKIII rear brake master cylinder?
After what you've been through, I can understand your paranoia about something being left out, but I think it came from something else.
I put a 70 set of cases together recently, I also did the AMR oil pump mod and also their recommended change to the timing cover oiling to match the later MK3 cover, the grub screw for that was 1/4 20TPI which looks like the one you have. There was no other grub screw any thing like it anywhere else on the assembly.
Can you confirm this is not something related to the tools you are using?