A customer comes in and purchases three official checks in the amount of $700, $3,500 and $6,000 in cash. Since the total is more than $10,000, we will complete a CTR. Since the total of the checks exceeds $10,000, do we need to document on a $3,000 Form? If it is not needed, is there any problem with keeping this information on a log form? Thanks for your help!

Can anyone respond?

The CTR is the only requirement you have. The Monetary Instruments rule is for instruments from $3000 to $10,000 inclusive. Documenting this on a separate log when not needed would only indicate a training issue - not a regulatory violation.