1998 Toyota Rav4 battery terminal removed while engine running

I am working on a 1998 Rav4 where the Battery Terminal was Removed while the Engine was Running to check the alternator. The car started malfunctioning (windshield wiper came on – lights flashed etc…)
The AM2 and SMS Airbag Acc fuses blew and no matter what I disconnect associated with these circuits they still continue to blow.
Has anyone else experienced this? I’ve been told it could be the BCM or ECM but I don’t know how to test for this.
Thank you,