I have command being upgraded to level 4, and most of the others to level 3 - think medical is level 2, and animal might just be building level 1 I think.
I extract pretty much everything I can find - and then sell all weapons and some vehicles and plants.
The easiest way to build resources is to keep sending troops out on combat deployments - there is a list of missions they can do - some are mainly cash, others can bring in metals etc. Once they have finished, then you can send them out again.
The other thing I do religiously is as soon as any soldiers join my base, then I check in the staff management and make sure there are no trouble makers - those I dismiss instantly as I can't be arsed with them potentially killing any specialist etc.