Not sure if this helps or not, but with regard to the problem with the Harrier GR-9 not sitting level at mission startup when playing as UK armed forces, one possible solution may be to use the CUP United States Marine Corps faction's AV-8b instead. It's the same aircraft but just has a different name (and different class name too). I don't know why, but the AV-8b doesn't seem to have the same problem with wing drop as the GR-9. If you add it to a mission in the Editor, it sits normally with wings level.
Of course, you don't want a Harrier with US markings when all the other friendly units have UK kit but there may be a solution for this too:
If you enter the Editor and add the AV-8b to the mission, you can then right click on the aircraft and select Edit Vehicle Appearance.
You then have the option to select the Camouflage button top left and choose UK Royal Navy...voila...it's now a Harrier and not an AV-8b.
Of course, if you're scripting all this, then the Camouflage option may not be available (I don't do much Arma scripting so don't know if camouflage is exposed in the API).
Anyway, it would be nice if the Harrier was usable in scenarios where the Base is an airfield...it would offer the possibility of flying above the range of SAMs and using LGB's against enemy armour, etc.
Apologies if you've already fixed this or found an alternative solution...just thought it was worth mentioning.