Welcome to EpoS Wizard!
Going back to your original questions;-
1) I think I'd look at using an ETAL script for this. You could use 'beforekeypresss' and pop up a number-pad, then either enter the over-write code or use a mag-card to do it.
3) As there is a separate M&M report within TouchPoint, I would guess these figures are available, but I`ve never tried to collect them manually from an external program before.
4) I presume Clerk 99 isn't set as a training clerk? What happens if you set it to 101 Clerks in file sizes?
WHOA Si - 
I'm from a hardware background. Writing scripts for me goes back to the '70s a dos program to work out the area of a sqare that's about it. 
Is this something I can order from ICR directly or do I have to find a third party "boffin"?
You could order from ICR, but if you ask on the forum I'm sure it could be worked out easily enough at no cost.
... Are you on the forum?
Yes, I have access to it through a company I sub contract for (I' freelance and tend to tart myself around a lot! 
)
I'll give it a go, once I ask permission from said company - cheers 
quick update - yes Si - adding clerk 101 did indeed make clerk 99 visible in samstock
not sure why but as its fixed, thanks for he suggestion 
