I'm scheduled to go into production next month. I ordered the 2.3 Automatic but I'm feeling Manual right now. Is this a modification I can make at this point?
You can ask your dealer to try by submitting a request to Ford. I'm guessing that you won't be able to because the transmission type likely affects the VIN.
I was able to add the sasquatch package to my order after receiving a VIN, likely because that package didn't have any change on the VIN and the parts must have been readily available.
Superficial changes like paint can be made for a while after VIN assignment, but I seriously doubt you could change significant components like transmission once you have a VIN. Honestly the auto will be better anyway so don’t sweat it