Looking for simple guidance as I have forgotten over the years.

Customer makes a deposit for $12,000, $9,900 is cash. Would I file the SAR for $9,900 or $12,000.

Any reference to FinCEN guidance/Reg would be appreciated too if you're familiar with it.

You won't find any written guidance. You report the dollar amount of the transaction(s) your institution considers suspicious. Do you consider the $2,100 in checks suspicious? If yes, report $12,000. If no, report $9,900.

Of course, if you consider the $2,100 in checks suspicious, you'll need a check box besides structuring to avoid CTR requirements since the check deposit wasn't structured.