In regards to the printer cartridges (thread 34241769), I'd agree that objectively speaking you didn't really steal anything. You found an arbitrage opportunity and used it to the mutual benefit of yourself and the corporation buying the cartridges for $3 each to refill/resell.
In the case of the business rewards, that corporation created a customer rewards system, and you found an exploit in the system (i.e. using the store/receipt number along with a programmatic search for past transactions). I think if you had used this exploit casually, the FBI would not even bother pursuing it, and it probably wouldn't have been detected in the first place. There is some level of acceptance you need to have in the fact that you broke the terms of service by creating thousands of fake accounts, went to many stores in many different cities/states, adapted the exploit (when they added purchase amount verification) by noting purchase amounts of other customers in the store, resold the benefits on eBay, hired an accomplice in New Mexico, and so on.
On a personal level though, I'm sincerely rooting for you - the amounts in question are a rounding error to that size of corporation, and the "stolen funds" in question were anyways intended for customer rewards. I think your best outcome from a legal perspective is to admit what the evidence overwhelmingly seems to indicate, be radically honest with yourself about the situation, and resist the urge to be combative on technicalities - consider how it may lead to a worse overall outcome.