I just ordered a new controller with delivery Monday. I was expecting to follow these instructions to get it up and running.
https://www.tormach.com/uploads/903/...0318A-pdf.html
Other then that I have no clue. Did it update the mesa card? Check to see if mesa card is seated also. Shipping can cause pcie cards to pop out.
I read people run Tormachs with Ethernet connections and I think with custom encoders from what I gather on linuxcnc. Guessing for rigid tapping or other secret functions