actually do have 3 Nema 17 motors already, the kit fortunately did come with this.
You entirely missed the point. The kit motors suck because they are designed to be used with no current limiting drivers. In other words, the coils are designed for exactly 12 volts square wave steps at slow speeds with very limited torque. Also, of note is high inductance. Basically, inductance is like inertia, things at rest want to stay at rest, so when the Mosfet switches on to turn on the coil, the voltage and current slowy rise over time before the max current (anf thus magenetic strength or torque) is reached. But, in a stepper motor, we move the magenetic field by switching the coils, so moving fast, the coil never reaches max current(torque) before we have to turn it off and turn on the next coil.
Point being, the motors I specified are higher current (2x) and low inductance, and have about twice or more torque. This matters because when you move the platform from a dead stop, the first step must get the entire weight moving and not skip a step (that nasty sound you get from the broken driver now). If you skip a step, you loose relative position and all motions after are off by some distance. This matters since we are trying to print one layer on top of the next=shifted prints (AKA ruined prints). I cannot stress how important it is to have the best motors. EVEN starting out, this was the cause of most peoples problems, because the Cupcake has many places to bind, especially the Z axis with 4 threaded rods. If you skip steps in z, the head doesn't move up, then drags the nozzle through the same layer and causes drag skipping the x and Y steps too. TOTAL DISASTER.
The quad stepper output holes are designed for screw terminals like these
https://www.sparkfun.com/products/8084 (you need 2 for each axis or 8 total)
now the other trick, the holes aren't spaced right for the .156" header 4 pin used to connect to the stepper motor connector. They are close, but the spacing is off and the holes are too small. Thus, it's easier to get the screw terminals, and then stick the header into the screw terminal at a right angle (sort of an adapter) to keep you from cutting the connectors off the wires and then dealing with wire order issues.
Actually, Digikey has these right angle headers http://www.digikey.com/product-detail/en/26-48-1056/WM4703-ND/26783 (your need 4) and, if you are good with solder, could maybe solder the bent leg, flat to the board over the holes, ensuring you got good flow through to both side of the board, but, that is a mechanically weaker setup than the screw terminals+header.
And then the inputs would be easiest to solder straight headers and then use female to female jumper wires (again, it's only 3 per axis) to jump the male pins inside the 10 pin sockets on the motherboard or the 5D shield (you really need to buy)
headers
https://www.sparkfun.com/products/116
wires (get 2 packs for good measure since 1 pack is just enough wires exactly)
https://www.sparkfun.com/products/8430
FYI technically, what we are doing is using a single board solution to make this http://www.thingiverse.com/thing:8586
It uses Pololu 4983s just like the 4 that are on the sparfun board, but they cost $13-14 each for each axis, and then you need the board kit, headers etc. Sure, these connectors we need cost a little too, but easier to get your hands on than that kit.
Anyway, if you got those parts and they are all in stock, a few minutes of solder, and you could be running.
Oh yeah, power for the quad stepper •2.1mm, center positive barrel jack
This would make life easy https://www.sparkfun.com/products/10287
Then this to connect to the power supply https://www.sparkfun.com/products/11298
You could just cut wires and solder, but I tried to give you nearly plug and play.
Also, just saw this. "it has an extruder mk4."
PM me, I have some older MK5 head stuff and a crap ton of Mk4 parts from when Makerbot sold them off in bundles for $9. If you get really, lucky, you could make a Mk4 last (I have one too that works, but low hours). Further, you really should get a relay to protect that expensive and not easily replaceable extruder board.
http://store.makerbot.com/relay-board-kit-v1-0.html
Directions to use the relay can be found in the cupcake instructions for the ultimate kit.
Point being, yes, I just gave you a long list of parts to buy. They all make a huge difference and some of them are just going away when the last ones are sold (5D shield, relay kit, pulleys and motors from Makerbot). You should no matter what buy the 5D shield. If you don't want to mess with the hassle of making and wiring the quad stepper as a beginner, I understand, you could just by the replacement stepper driver http://store.makerbot.com/stepper-driver-v2-3-fully-assembled.html . I also would get the $17 relay board from from Makerbot Point being, that last list is a good bare minimum I would buy to get this fixed, running and upgradeable for the future. You can run the old motors, and the old stepper drivers and get by, just the machine must be close to perfect. Upgrading to 3 of the new motors would make life easier starting out when you likely will have binds. That's at worst $63 upgrade but so worth every penny.
The point is, the upgrades all make a huge differnce in how the machine works, how good it prints, how many problems you might have, and since you are starting out, we already know all the fixes, thus you won't go through half the frustration we did.
