I figured out a hacky way to get it to work (for me, at the very least).
After running recompile.bat and reobfuscate.bat, look for a folder called temp. Inside the temp folder, you will see a jar called client_reobf. If you open that up with 7-zip or WinRAR and pull out the folders that contain your code (starting with the uppermost folder of your package, so for me, "conventnunnery"). After pulling out that top folder, put your texture files in and then zip it up. You should be good to go.