Hi Zak
I dual print a lot, and have spent 1000s of hours trying to get consistent perfect prints, I have come close but have never achieved consistent perfection. I have printed with a Duplicator 4s a Flashforge Pro and a Makerbot Replicator 2x and even a self built Delta Rostock with a 4 nozzle Kraken. I have used Makerware and simplify3d, they all exhibit this problem. I have used all sorts of material combinations and same material dual colour combinations, like you are doing.
The rags you are getting can be reduced, but not eradicated, believe me I have tried all the stuff other posters have tried ie increasing the retract value- in simplify 3d this is a setting, also by the way in the new Makerware this is now also a setting, the previous poster is right- in the older versions of Makerware you would edit the retract in the extruder profile which is quite a fiddle, but in the new version it is now a lot easier and can be done in settings.
Reducing the extruder temperature will reduce ooze, but really it would have to be done on the hoof to be effective and since it would take time to reduce the nozzle temp to below the materials melting temp and heat up again is impractical, and cannot be done in simplify 3d as the previous poster intimates. Also even with retract at extreme distances there is always a small amount of material smeared on the inside of the nozzle which will ooze as there is no negative pressure sucking it up during retract, gravity inevitably pulls it out, and I have noticed the longer the printing nozzle works the more oozing comes from the other nozzle which is what you would expect and is the root of the problem even keeping temperatures low fails because of this, this is why the pictures of the calibration cubes look clean, basically the material has not had time to ooze because the cubes are small, however bigger prints suffer badly, so to be of use you would have to print a calibration cube close to the size of the target print, but then you may as well just print the target anyway. I would say from observation as a rule the longer the time between nozzle swap over the more rags are produced.
Making small sacrificial areas does not work for obvious reasons. The purge walls help, but do not work 100%, it can still happen with all these tweaks, and even a couple of rags can spoil a print.
I fear us dual 3d printers will have to wait for the next generation of printing machines which are just around the corner these mechanically shut off the nozzle with a retracting pin, so stop ooze completely. So far I have seen only two machines like this the Arburg Freeformer (very expensive), and the soon to be released dual headed Celrobox to be shown next month at TCT in Birmingham UK, price not released but I believe around the £1000 mark. I am going to give it 6 months for this machine to be bedded in then sell my old tech and move to this new tech, however one question about this machine is while at the moment I know for certain the single head version uses this technology, I am unsure if the new twin version will, I assume it will but until I see it at TCT dont take my word for it please, but worth checking out Zak.