Did you try what the original poster did? Uninstall everything (including unity) and reinstall just jdk, android, and godot?
As a workaround, you could boot up a linux live-drive and export from the linux version of godot. I'm not having any problems with custom builds. Unfortunately, you'd have to download the android sdk files for linux before attempting it. On the other hand, if the problem is the libraries you're putting into your custom build, this won't help at all.