I am sorry that I don't have any suggestions either. I am also worried because I might be in the same boat as you (need to change the markup since we have to get PCI compliant).
Do you have any traffic statistics that you can post here pre- and post-your markup update? What does the google referred traffic look like for your top 10 pages before and after the change?
And can I ask how you are tracking your major keywords?
and are those keywords primarily one-, two-, or three or more words long?