Stepper Motor Troubleshooting

If a motor coil is out of phase like that, it can only be one or two steps, maybe less, away from being 180 out a phase, a condition in which it won't step.  Try switching these round. 

Sorry, switching which pins? The two crossed.

Yes, interchange them.  If this is the problem interchanging the other coil would also work, but the motor would run in reverse of our expectations.  If your axle jounces around, pinch it slightly between the fingers of your cotton-gloved hand.  Some motor-driver setups resonate when they are completely unladen.

Ok what I have done is jiggle the molex pins to get them to make contact better (of course the solution is to jiggle something). As a result, I can now get the motors to run in the proper increments, no unusual noises or anything, but only in one direction. Switching the two crossed wires switches that direction.

This is what you are going for.  Notice how only one coil changes per step, reminiscent of Grey codes.  Going backwards means going -1 step.

Great. Now, how do I get it to run backwards as well? BTW I'm using Repieter Host's manual control function to run the motors.

This is going to take some detective work.  Perhaps your driver is not able to do everything it should, somehow able to step in one direction but not the other.   If you are using proven software, it is less likely, but not impossible that you have a software problem.  We need some way to visualize the current through the coils to see what is happening, alternatively we can make guesses.  Here is a good article on stepper motors:  Stepper Motors - Introduction and Working Principle

Here is a cheap way to get a little idea of what is happening to your SM.  Each diode string consists of an LED and a reversal protection diode.  LEDs do not have good reverse breakdowns, so use a hundred voltish signal diode in series.  Use different colors.

Ballast resistor can be Kish if dim, reduce (increase conductance)

Dinner calls.

Any type of resistor or LED your recommend? I got a few laying around that might work, otherwise I'll have to get some.

Just use any old indicator LEDs, for the ballast try approximately 1K, any type will do, quarter watts if you got 'em.  A couple of 1n4003s for the back-up diodes would be more than adequate.  You can degenerate a bipolar transistor into a diode by connecting the collector and base terminals if you have those laying around.  Almost anything will do.

I'd make it so that a red LED lit when coil A was energized in the positive direction.

I'd make it so that a blue LED lit when coil A was energized in the negative direction.

I'd make it so that a yellow LED lit when coil B was energized in the positive direction.

I'd make it so that a green LED lit when coil B was energized in the negative direction.

But, of course, it doesn't really matter.