you need to replace the bob (break out board) with one that's pp or Ethernet (not the nc one its *********) get something that is made to run with M3 or M4 it will make life a lot easier something like an ESS to a bob or just a bob.
getting a bob with Ethernet is the best way to go for future proofing your machine others will disagree I am commenting on what I have done.
there are a lot of ways you can do it it just comes down to money.
I rebuilt one machine with an ESS to a mb06 bob to gecko drivers it works very well, (when it wont s to I have an earth fault in my shed somewhere that's a different story all to getter)
also check that the steppers are what they say they are I had miss labled steppers it took a long time to work that out.
your wiring is more than like non shielded wires it would be a good idea to replace your wiring with shielded wires my opinion.
I get a lot of parts from
http://www.automationtechnologiesinc.com/ I just email them my requirements they recommend what I should get they have been correct every time for me.