hi Richard,
Ok, the gold nut basically should only be undone is short quick changes as when you normally undo that nut the ink starts going back towards the carts. Basically inside that nut is a very very small black o-ring (rubber ring), this seals to the damper (plastic bit with ink in it). It sould like you have a JV3-S and not a JV3-SP, so your cyan and yellow are shared with the same head.
If you look at the pumps (hidden under metal cover under heads) you will see that there is pipes connecting out to waste, you should be able to break these pipes (connector) and attach a syringe (medial supplies) to it, might need to find some spare tubing somewhere, depends on pumps. What we do is place heads over the capping station (normal docked) and then suck the ink through the heads (gently) with the syringe, this brings through the ink from yellow and cyan heads. However if you are feeling ease at pulling a syringe back, you have an air leak.
So, air leaks are caused by missing o-ring in cap.
Dirty heads (crap under heads) over capping station (bad seal)
Bad alignment of heads (not likely)
If you can feel good suction and ink going into syringe then seals are good and likely to be your pump is broken and cannot suck air through well enough. There might be visible signs of a broken pump or different clicking noises then normal. You could swap pump pipes to check with a good pump, check what you are doing first.
Another thing that Does call ink to mix, is leaving it to soak for more then half and hour, the fluid goes up the heads so all you do is keep printing until it prints normally. However the syringe method helps.