Hello Ramon, welcome to the forums!
Bug 1: the bazooka infantry (aka missile defender) has that bug, try making it's weapon, 'MissileDefenderLaserGuidedMissileWeapon', setting these two lines of code:
Code:
AntiAirborneVehicle = No
AntiAirborneInfantry = No
if it is there, change it; if it's not, add it.
As for the fuel air bug, not sure how to fix that. It might be due to something that the AI does since human controlled fuel air bombs never act like that as far as I know.
To change the AI to rebuild the command center, you'll have to use worldbuilder. Since I never even opened worldbuilder in my life, I can't help you too much.
But you can check
SDI for scripting tutorials to help get you started in AI scripting. Although the SDI is no longer an active site, the material is still holds is valuable.