As you have done AP, starting point is 4.12.2, however you get to it. Then apply Modact 5.3 only. Then it has to be module 1, which is the maps that all the other 3 flight eras use.
Then module 2, module 3 and module 4. It doesn't matter which of the flight era modules goes first, they are all optional and totally separate from eachother. Just make sure the separate module parts go in order and yes, you overwrite any files that the installation asks to be overwritten.