I am now working on putting it all together and ran into some confusion when setting up the power supply for which I cannot find much information on within the guide. Could I connect the 5V at pin 2 of the RPi to both the H-Bridges to run the stepper motors or will I need to look at an external power supply for this? If external, what could I use? I have seen examples of 4 AA batteries in series, will this do the job?
I'm not familiar with the raspberry-pi, but there's a good chance the stepper motors draw more current than the GPIO pins can supply. It's better to supply these motors with their own power supply.
Depending on what voltage your motors require, you can use AA batteries. If the motors require lots of current, you may be better of using a LiPo battery of the appropriate voltage instead.