have been told that we must list all cash sales of Neg. instruments 3 to 10k. Should the sale of Bonds be included on these logs?

The only requirement is cashier's checks, traveler's checks, or money orders.

Sorry I don't have a cite for you but I do not believe savings bonds are included in what must be reported on the logs.

That's correct. Bonds do not meet the definition of 'monetary instrument.'

The requirement is to maintain a record of certain information on the purchase. Instead of a log for every branch, I have seen banks use a form to capture the required information and then the form is maintained in a central location, usually by the BSA Officer who also oversees the monitoring of the large cash reports.