If you find they're relatively close from these testing, then the KISS approach would be to connect them and treat them as one large bank.
If they're not close, then I'd probably treat them separately as two different banks of AH's. (Adding one of those fancy switches you mentioned, would make this much easier to swapping cables:)!)
Using and managing them as separate banks, you then know for sure how each one is doing, as well as you can optimize the charging for each bank.
Looking forward to what you find out after they rested:)!
Best,
Smitty