Just ignore the .DS_Store file, it doesn't do anything. Mac OS automatically adds that when you make a .zip so that if you decompress it on a Mac it knows where to put the icons. If you can't load ships on the pad, you may have to delete the kethane.cfg from your save.
Yes, you will. It looks at all resources. Also, this unfortunately means that you cannot currently build a rocket with SRBs in resource mode, as there is no way to get the SolidFuel to the launchpad.
It's possible, but I don't know why that would be. It uses the same function as the game does to show that list, so if you can access it from the game you should be able to access it from EL.