Just as with the Extruder Controller, the Thing-O-Matic stepper motor driver boards derive their logic supply from the +12 V line through a 7805 linear regulator. While that works in the ideal case, it makes the logic supply vulnerable to glitches induced by motor current switching.
This modification gives the stepper controller chip a clean +5 V supply from the Thing-O-Matic’s ATX power supply, by the simple expedient of removing the 7805 regulator chip and connecting the +5 V from the power supply Molex-style connector to the circuit pad that was the regulator’s output pin.
This is what the modification looks like on the PCB layout.
Use solder wick and a big soldering iron to de-solder the connections, then yank (gently!) the regulator off the board; you can see the outline printed on the board near the lower-right corner, between the two blue capacitors. This picture is rotated half a turn from the PCB layout shown above.
Connect a jumper from the Molex connector’s +5 V pin to Pin 3 of the 7805 regulator outline. The wire can be any size, because it carries minimal current to the driver chip’s logic circuitry; I used a strand stripped from a ribbon cable.
Put the wire on the bottom of the board, because the connector pin isn’t accessible from the top and the traces at the regulator output pad are on the top where they’ll be easy to solder.
Repeat for all three stepper motor controller boards.
Reinstall in your Thing-O-Matic and rejoice that nothing seems to have changed. This modification should reduce the number of weird motor-control problems, although it will not prevent lost steps due to mechanical overload or excessive traverse speed.
The Smell of Molten Projects in the Morning 
For those with less experience at desoldering, they might want to first clip the 3 leads of the 5V regulator so they are effectively desoldering (3) one lead parts rather than one, three lead part.
I’m asking you because you are more likely to have frequented the thing-o-matic forums, but do you have any idea why they would have added a 5V regulator when 5V is already available on the connector?
The only motivation for not clipping those leads is that you can solder the regulator back on the board if you change your mind. Of course, cooking the PCB while extracting the regulator would be a Bad Thing.
The regulator removes the requirement for a +5 V supply if you want to use the board in another project: just run everything directly from the same +12 V that drives the motor. I suppose that counts as planning for the future, but I think it’s suboptimal right now…
for my nickel, easier to just desolder and lift (or dyke out if you appreciate how few pennies a 7805 goes for) Vout and abandon the part in place… but i’m lazy.
Many of the Thing-O-Matic readers don’t have a bunch of electronic parts, so I figured I should conserve the existing part… and it could also serve as the seed crystal for a Parts Heap!