Deploying flaps after landing won't slow you down, in fact they will give the wings more lift. By pulling them up the plane should sit more heavily on the ground, making the wheelbrakes more effective.
Without trackIR there seems to be no difference, mouse controls head movement as before. Concur with the LMB shooting issue though. It seemed that occasionally clicking again would stop it firing like it was toggle but otherwise those guns just kept firing.
Um, do you mean you can't use the UHF when you've ejected. That would be because you're violently seperated from said radio by a whole load of rockets.
If that story was just a bit of background then try unticking easy communications in the options menu.
Epic thread resurrection. This isn't needed anymore as there is a "land" advanced waypoint action where they will touch down, leave the engines running and after the set delay take off again.