I'm not sure how I went and did this, but G1 X0 Y0 puts the left extruder at 0,0. I've tried reloading memory, doing this in g-code terminal M206 X0 M500 and power cycling I'm printing from each head just fine, but to get the right extruder at 0,0 I need to use MOVE AXIS and go to -38,0
I misunderstood this page and followed the incorrect instructions during setup: http://wiki.e3d-online.com/wiki/FAQ