FWIW, there is a table for gear determination thresholds in the map; I'm assuming that's specifically dealing with the gear indicator on the dash for manual cars, because it doesn't seem to do anything on my A/T.
Theoretically you could just calculate the percent increase between your new final drive ratio and the stock 4.1, then increase the values by that percentage. Someone with a manual should test that out to see if it actually works that way.
