[Kube]

In 1941, the program to obtain a Mercury engine and have it installed in a Ford was made official. Prior to that (1940 models) this program was kept rather secretive.
Thus, in 1941, there were quite a few Fords built with a factory installed Mercury engine. Quite a few but still, not many relative to how many total 1941 Fords were built.
The model number of your car remains the Ford model designation. The serial number was supposed to reflect the Mercury engine, IE the 99 prefix.