My wife and I filed separate but married last year and we are filling a joint return this year .. For my AGI for efile do I enter one of our AGI’s or combine the two?

You should be asked for two e-file PIN codes, use each of your AGIs separately. 

It is only showing one pin 

Are you sure you correctly indicated a joint return in the personal section?  I believe 2 codes should be required.  

@VolvoGirl @DoninGA