Ignore this post, the problem ended up just being solved by checking the step low active option in the ports and pins settings in Mach 3.
for anyone who may come across this post in a search of help, if your having trouble. the linked schematics are helpful, this is picture of my wiring setup http://i.imgur.com/DyBoN.jpg I jsut added a bypass of the e-stop. and here is a video with accurate wiring as well [ame="http://www.youtube.com/watch?v=XFCJtXcW8t4&feature=related"]veliki steperi se okrecu - YouTube[/ame] and he goes into a good amount of detail