set_clock_groups vs. set_max_delay/set_min_delay

Are you sure the issues are related to the gray code counters? (Every design has gray code counters crossing domains...) The fitter does naturally pull them together just to reduce routing resources used. Something has to go drastically wrong for them to get a skew greater than one clock period. I've attached a .tcl file that analyzes the gray code paths in FIFOs and can be used to analyze skew on other paths you set custom. It only runs in TimeQuest and doesn't drive the fitter, but can help determine if there's a problem. (It also doesn't take clock skew into account). Hopefully it helps determine if you really have this problem or it's something else.