If a bank has a possible FinCEN 314(a) match, should questions be directed to the specific individual and agency requesting the search as opposed to contacting FinCEN?

That's how I handled it when I had a possible match recently. I contacted the agent and he helped me determine that it was not a match.

The instructions on the form indicate to contact the referenced individual(s) on the form if there is a possible match, and FINCEN for other than matches.