So I tried this and came up with some interesting results. This worked, but not on the stepper motors I intended to use.
The steppers I got working have a 50 ohm winding, 6 wire, and I am leaving the center taps of the windings open. They are pinned out differently, where pins 1 and 3 are one winding, and 4 and 6 is the second winding.
The steppers I initially tried are also 6 wire, but only about 4-5 ohms. Much higher current draw, and are the generic 3d printer nema 17 that I have been using for a year or so. They are more powerful and smoother, but would not run. These also have the center taps of the windings left disconnected, and have coil pairs at pin 1 and 4, and 3 and 6.
Both are nema 17's, and when testing I am indeed flipping the two center wires when switching test motors.
At this point I am successfully moving the machine, but only with the spare older motors.
I'm pretty confused now. Is it still a timing issue? Are the steppers pulling too much current from the drivers? I am feeding the board 12.5 volts at a max of 3.5 amps on my power supply, but it's not taking that much current. Not even close.