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Sorry about the wait, things have been pretty hectic recently, done with all the tests now, though! Hm, well that is bizarre... Did things run properly when you used the original firmware and the original wiring diagram instead of the altered software/wiring methods? Or are you using your altered firmware because the original firmware wasn't working for you?
For direct axis movement, I use Pronterface, which comes in the printrun zip downloadable here: http://www.pronterface.com/#download