Hello!
Transiting in CMN is quite smooth and I don't think you will have any problem.
You mention two different tickets (JFK-CMN-RAK).
~ I would double-check if you can be checked-in for both flights so that you get a BP for both flights from JFK. In that case, you will clear pasport/customs in RAK. Arriving in CMN, you will go through security check for the domestic terminal. That is quite small with 9 gates next to each other. There might be a small lounge (def. no showers) for status/biz pax (not sure) but as Y pax you won't have access (arriving in C does not matter). Sometimes AT operates AT7 i/o 737 for the flight and they might have more limited cargo but I don't think that's a real issue to worry.
~ If you don't manage to link the two flights, then it might be more complicated: you will have to clear customs/passport in CMN (you will have fast track due to C arriving pax). Then you will check-in for your domestic flight (small walking distance from arrivals to check-in). You clear security (+passport) and you will fly to RAK.
For lounge, indeed
access to AF lounge is provided.