To take weapons off your wingmen; in the weapon selection screen click on one of your wingmen's ship, then click-and-drag their weapons out of their secondary bays. Or put something else into their secondary bays, like hornets, and the Cyclops (if they have them) might go into the weapons pool. I should note that I'm not sure this will work, because I'm not sure what FSO's behaviour will be in this situation! It may still refuse to load the Cyclops onto your ship.
To add the modified mission, go to the location that the mediavps are stored in (assuming you are using the mediavps!). That should be a location like KNOSSOS_FOLDER/FS2/MVPS-3.8.1. From there, create two folders, data & data/missions. And finally save the modified SM1-07.fs2 file to that location. i.e. the full path to the file should be KNOSSOS_FOLDER/FS2/MVPS-3.8.1/data/missions/SM1-07.fs2
Lastly, I couldn't see a new attachment with both your pilot files?