So we got everything moved out to the garage to make some first cuts. Plugged everything back in and now are unable to manually jog the machine to its full extents. It will jog by 200 in x or y in repetier and then go no more.
On a side note, when we tried running a new program created in fusion 360 the gantry moved at a crawling pace despite all settings we could find being ok.
We do have endstops connected.