If you have removed .002 from each side of the rod and you now have .003 clearance, it must have been quite loose. Usually a knocking bearing will leave some evidence. I would check all the rest. If you have .003 now, it may run that way without knocking. However, if you had the rod machined to take an insert, you could try a .001 under for a trial fit. Kanters sells standard, .001 .002 and some incremental undersize.
