I assume I would do that by swapping the pins around on the connector?
I noticed in the schematics there is an S1 and S4 jumper that is associated with single side or double. If they are open they are single. But I'd have to cut the trace on the board to open it. Thoughts?
I would NEVER swap the heads in this situation. The erase coil with too low resistance could easily damage permanently the driver which is mostly in the U11B hybrid and you'll have a dead drive as a result.
I don't know how the firmware reacts to those S1 and S4 cut, I've never seen a 1001 in real life. I'd try cutting them and disconnecting the green wire going to the top head. If it starts working as a single side drive, you have something still useful.
Frank