I haven't been in that situation before.
If it were me, I would just hook the batteries up and go. IF you think things are not going well, then take the batteries off line, wait 45 minutes to an hour, (allow ECM to forget a few parameters) disconnect the EZ and drive for a day or two. Put the EZ back on when you feel all is well.
Marco would have the skinny on whether it would make any real difference. Why not PM him?