1. What's stopping less scrupulous species (such as the Ferengi) from bypassing the UFP and making First Contact whenever they want to (say, to exploit planets)? Does Starfleet militantly guard pre-warp civilizations? I'd think that would require more ships than even the huge Starfleet possesses. Or does the UFP only assume responsibility for making FC for planets within its own territory? Obviously it can't go all over the galaxy doing this. So does it restrict making FC to planets within its borders?
Pre-warp planets within it's borders, without a doubt (though that may include warding of pesky civilians, including Federates, more than anything). As for thouse outside, I'd say it tries to protect those that are nearby, in it's own 'sphere of influence' so to say. Of course, as you point out, resources are limited so sometimes it'll have to pick and choose (based on factors such as the pre-warp civ's need for protection and the Federation's own interests) and sometimes to provide protection only on a semi-regular basis. But it's also possible Starfleet personnel have a standing order to try to prevent foreign meddling in all the cases they come across, wherever they may be.
The argument could be made that Cochrane was only performing final assembly and launch in that silo, possible for security reasons and that research, development and production of the Phoenix and the warp drive was actual carried out in the central area of the nearby (former?) Air Force base.
Yeah, that's the rationalization I always use. For all we know, most of the work was done before WW3 and then the war devastated everything leaving only Cochrane and a bunch of his associates to improvise the final touches.