Re: transmission losses
If the transmission has a locking torque converter, I doubt there will be that much difference. The ford C6 HD tranny for example (open TC) is what I call a "fuel eater", the lighter duty AOD (locking TC) is much better, but an auto tranny still has to build fluid pressure to activate and hold each gear, so there will still be a disadvantage compaired to a manual.
From experience, I haven't noticed much difference in MPGs between auto and stick, becuause auto can keep engine RPMs more consistent (torque converter makes this possible), but consistency doesn't matter very much with elecrtic motors, so I suspect the manual is still the better choice.
Something else to consider, is that an automatic cannot be put in gear unless the imput shaft is already spinning, because the hyraulics have to start pumping first, but there also isn't very much holding force actually applied to the internal clutch packs at idle, so there may also be a problem if you try to take advantage of all the low end torque that electric motors are usually blessed with. This would also imply having to "idle" your electric motor.