4EAT Transmission swap help.

[Gmimpreza]

I just pulled the transmission out of my 2008 Subaru Impreza 2.5 non turbo. I recently sourced another transmission but there is a few slight differences. The new trans has a 3 bolt shifter switch and a 12 pin connecto, the trans pulled from the car has a 2 bolt shifter switch with a 9 pin connector. The new trans also has the external filter and the old one does not. I was just wondering if this swap would work, because it looks like the connectors will still plug in despite the extra pins. Or will it just throw codes and make the ECU and/or the TCU freak out? Any help is greatly appreciated.