^If you coded it properly the DME and DSC don't look for the EGS which is the auto trans computer. Probably will need to be recoded if you haven't done it already.
I'm in the process of this swap right now and am just waiting on my driveshaft... I left the entire auto harness where it was and just tucked and ziptied the trans connector away as to avoid any grounding issues. I'm doing it on an N55 and using a 2009 N54 manual trans. I was able to start the car up without coding anything yet so that's a good sign to me
hoping the driveshaft comes tomorrow.