My mechanical testing hit a small snag recently. One of the threaded rods refused to play nice with the carriage plate. Turns out that the plate (the one which has the x motor attached) wasn't parallel to the gantry and the rod needed to run at a slight angle to the nut block. Despite using a flex coupler there was a fair bit of noise from the rod/nut interface.
After 3 days of disassembly and reassembly I eventually shimmed one of the gantry uprights in order for all the v-wheels to make contact and for the x axis makerslide to sit correctly on the carriage plates. If things aren't properly lined up with the bolts loosely attached, the plates will not sit correctly when the eccentric nuts are adjusted and everything tightened down. My small assembly tip: clamps like these
http://www.irwin.com.au/tools/browse/clamps/hand-clamps are fantastic to hold the x axis up during assembly.