I am sleeving my PSU and somehow managed to get the pin order of the EPS12V 8-pin +12V connector mixed up. I know which sides the 12V and grounds belong on the connector, but am trying to figure out if the actual order of each color wire matters. From what I've gathered there is both 12V1 and 12V2 rails present, so I'm not sure if they can be interchanged with other 12V pins. Likewise, does order of black ground wires matter?
Well, internally each "power rail" is actually coming from same source, but each has its own current limiting, so it may matter. Basically PSU designers may have connected the two rails with least load to the connector and using another cable may connect the processro to a rail with heavier load which can make problems with overload protection. For example, it could happen that you connect wires which share same current limiting circuitry to video card (or some other big consumer) and processor and that could cause problems later on such as unexpected shutdowns.
As for black wires, again it depends. If they are directly connected together in the PSU and aren't monitored by current limiting circuitry, then there should be no difference among them. Otherwise, you could expect some problems to show up, again related to current limiting circuitry not working correctly.
You could open up the PSU, if you feel comfortable with that, and trace the wires themselves with a multimeter and find exactly where each wire goes, just to be safe.