For some reason, when I manually move the y axis, or do auto home, when the carriage is near the front of the printer, a weird single clicking noise is made from what appears to be the upper right side of the printer. 95% sure it is coming from bearing or y axis rod on right side of printer.
Probably not, just will give inconsistent results (y-motor skipping incorrect dimensions etc) Juyst redo the Y-Axis alignment from wiki.... http://wiki.e3d-online.com/wiki/Printer_Commissioning#.281.2.29_Y-Axis
As Mark says, it is unlikely to be a problem other than possibly causing uneven movement. Do go back and check your commissioning for the X and Y axis and tighten the rod and bush clamps carefully afterwards; it is important to check the tightness of the frame screws beforehand and to move the Y-carriage to the end of its travel towards the mount you are doing up. You will need to do the tightening on all screws and clamps frequently over the first hours of regular use, as the plastic "settles" gradually over time, which is a common problem with 3D printed parts that have a relatively low resolution, such as these.