In my mind the big issue underscoring all your potential problems is requiring a certain level of knowledge, skill and understanding that (no disrespect) your staff may lack.
How do you envisage the workflow - will you have the time and resources to oversee every repair yourself from initial assessment to checking and signing off? It sounds like you'll need to micro-manage your staff to ensure they remain on the right track, and will probably have to provide a lot of training at the least, and do some of the more complex tasks yourself. Of course being safety-critical you'll need to do a rigerous check-over pre-sale to ensure your arse is covered.
I can't offer a whole lot in the way of answers to your specific questions, other than to suggest that really most can only be satisfied by experience. Initial assessments of value can be carried out on the basis of
ebay sold prices plus the cost of any work that a bike needs, and over time (if not already) you'll get a good idea of what's worth saving and what's not. I would caution you to give the benefit of the doubt to old steel; the practical value of which might not nec. be reflected in its market worth.
What's the main source of your bikes - donations from the public? If so I guess you'll mostly be looking at lowish-end stuff, probably with a fair vintage element. Obviously you'll need to make a judgement call on the numbers; free labour will help but the cost of service items can quickly add up (take my Raleigh for example - cost me nowt, owes me about £60 in mostly consumable but I think I'd struggle to get that back if I tried to sell it).
I think once you've written off all the non-viable crap (cheapo modern BSOs that require more than just a few consumables etc) you'll probably have a fairly narrow spectrum to work within.
Good luck - it sounds like a commendable project and I'll look forward to hearing how you get on