No, as you can see from the pololu schematic in #10 the numbers 1 und 2 refer to the coils respectively. So the connections should be ok.
Are the color connections really from your motor? There are motors that look very similar, but have a different pinout. Is a type number printed on the motor? Can you post a datasheet of exactly the motor you are using?
See post #21.
You have:
1A RED
1B YEL
2A BLU
2B ORG
You need:
1A RED
2A YEL
1B BLU
2B ORG
@wildbill @xfpd The motor very much did not like the Red/Yellow being on 1A/2A and Blue/Orange being on 1B/2B. The motor became hot very quick and something seemed to blow on the board, not sure what yet...
@MicroBahner The screenshot I attached is a snip from the stepper motor drawing. This is the full data sheet which includes that motor drawing. Datasheet (rs-online.com).
I was trying to do some fault finding earlier, and when the motor was connected like this picture, disconnecting 2A/2B and leaving only 1A/1B connected, the motor started rotating (was still jumping/juddering) for a quarter of a turn then went back to twitching. If I forced the shaft back round again, it did the quarter turn again then back to twitching. I'm thinking that one of the boards may be causing the issue so have ordered a MikroElektronika Stepper 2 click for A4988 as I can't seem to find the one I currently have and see what happens.
If you remove the motor wires from the terminal block (and remove power), the shaft should easily turn. If you twist RED/YEL together, you should feel resistance in turning the shaft. Same for BLU/ORG. The wire-pairs with resistance in movement are coil pairs. You could also use a multimeter to look for shorts, now that something (might have) fried. Same-phase on two pairs will be zero-ohm... but if a third wire is zero-ohm, there is a coil short circuit. Sorry if that is the case.
Could 1/8 microstepping be the issue? (assuming zero-ohm jumper = 1). Two bits of de-soldering could bring it to full stepping.
@xfpd Yes, connecting the RED/YEL and BLU/ORG together does cause a resistance. Tested with multimeter and getting 4.2 ohms.
Looks like is what has fried 
I can smell it from here. Overcurrent in a stalled state? Be sure to adjust the current limit when you get a new module.
So your custom shield with the pot and all the hard work trying to figure out how it worked now goes into the trash.
Do you have a pot you can use?
Do you know how to connect it?
Don't forget to buy a new capacitor
