What constitutes "higher-amount transactions" in your MSB risk assessment? We know they are cashing check over $1000 in order to be considered an MSB (unless they only do transmittals). Maybe greater than $3000? $5000? What are other banks using as the threshold?

The threshold would depend on the MSB and your own procedures. There are MSBs that are allowed to cash checks up to $100M. Others have limits of $40M or $50M.
It depends on the areas they serve and the collateral that the bank is holding for that activity.
When accepting an MSB as a customer you would get your profile of expected activity. Most banks are holding collateral in the form of a CD on MSB accounts. The amount of the collateral would depend on the expected activity and the dollar amount of the checks that they cash.
You would monitor the depoists for these high dollar checks and reserve the right to increase the amount of the collateral if the checks are higher than anticipated.