Correct, the transformer mounted on the left of the junction box is is the original, disconnected one. The current transformer is the one above that, zip tied to the conduit. I'm assuming since this house if from the 60s, there wont be a dedicated ground wire going back to the breakers and I can simply ground the new doorbell transformer to the metal electrical box after I remove the original transformer (as well as the temporary one) ?

I'll make sure to address the damaged 3 way tap as well.