Dave,
I fear you've overcomplicated things greatly...
2) PhoneGap Desktop App is intended to /serve/ applications to the PhoneGap Developer App. It reads to me like you're trying to do the opposite? Leave the desktop app out of it for the moment. [But this is why it only lets you specify a port -- you're specifying which port on localhost to serve from, not which address to connect to...]
3) PhoneGap CLI has "phonegap serve" -- this lets you also serve an app to the PhoneGap Developer App. You can use this on Windows, Linux, and Mac OS X.
So for development, you could stick with your Yosemite VM for now or use Linux. Either way, my suggested setup is the same:
a. PhoneGap CLI installed
b. "phonegap serve" from your app's project directory
c. On your iOS device, launch the PhoneGap Developer App
d. On your iOS device, enter the IP and port number of your machine (if using Yosemite VM, use the IP assigned to the VM)
e. Test. Editing files within the app directory should automatically reload the app on your device.
To /distribute/ your app, you'll have to have to do that from Mac OS X. Since you have a working VM, you should be good.
NOTE: The Yosemite VM is NOT a supported method for iOS development. Apple's license permits it only on existing Mac hardware, so chances are pretty good you're violating the license. Deal with that as you will. From a technical perspective, you may have issues with system updates and the like, but as long as you can keep it up-to-date, it should function just fine -- just out of the license scope.
You've also mentioned ios-sim -- you can start a simulator using Phonegap: "phonegap emulate ios" from the project directory. You still need ios-sim installed on Yosemite, but it's easier to start it up IMO. Do keep in mind that the simulator does not accurately reflect the app's performance or feel -- you must install it on a physical device to ensure that it works the way you expect.
Hope that helps...