If you install the F14 cockpit and fly the F14, you will indeed see the F14 from outside as well as seeing the F14 surfaces when looking out from the cockpit. If you fly the F14 WITHOUT the cockpit, you will see the F14 in outside view, but when looking OUT from the cockpit, you will see F/A-18 surfaces. The views of the aircraft from inside are part of the cockpit art.
Not sure about flaps, but movement of Gear and Wingsweep (and Tailhook) should be visible. The Wingsweep, however isn't dynamic as a function of speed as in the real jet. I believe that the wings sweep forward when gear is down, otherwise they are swept back.
There is no manual control of wingsweep.
If you fly the F14 as a Human, select one of the F14's with (MOD) after the name, and use the F-14(USN) for AI.