Assuming you are using our package name (edu.mit.appinventor.aicompanion3):
Build your new Companion. As Evan has said, remove the android.sf and android.rsa files as well as everything under lib (the large files that end in ".so").
You can sign it in two different ways:
1. Jarsigner: Use the java jarsigner tool using your android.keystore file to sign the edited Companion. Then use the "zipalign" tool from Google to align the file.
2. apksigner: *first* use the "zipalign" tools to align the file and then use Google's "apksigner" tool to sign the Companion
After you have done one of the two steps above, start the emulator (you can do this from App Inventor itself). Make sure you have the Google "adb" tool installed. Then once the emulator is running do:
"adb uninstall edu.mit.appinventor.aicompanion3"
This will uninstall our version that comes with the setup tools and is signed with our key.
Then "adb install <whereeveryournewversionis>"
This should install your version of the Comapnion. Then restart the emulator and you should be running.
-Jeff