I must confess I did not read the whole post. But since it is an issue of getResourceAsStream, if you but your properties files into the res directory, then you can access them via
getClass().getResourceAsStream("/firstFile.properties")
for example.
I have never used the MicroEmulator (never even heard of it, but this might be my slip), but this should be a general rule. Once you packaged your application into a jar archieve, you should be able to access your properties files like I mentioned without any problems. In the emulator it works, on a real phone it works, so you should be ok.
When you are usign the method above, the "/" specifies that you are already in the resources folder, so any consecutive folders, like
res/localization/english/enFile.properties, can be accessed by using
getClass().getResourceAsStream("/localization/english/enFile.properties")
Mihai