Alright, here's how it went down. The header tank / coolant hoses weren't changed over as it isn't needed apparently. They did flush it through twice and road test it. The ford service boys ASSURE me that some residual fluid is completely normal and will have absolutely no negative effect on the cooling system. It is only in the cooling system, not the transmission lines, and all the oil was flushed out correctly, it's just residual from the hoses. They have guaranteed me that it is not a problem at all, you just have to drive it out, they have seen it many times before. I insisted that they take it again tomorrow and give it another big flush out just for piece of mind, since I'll be going on a 2000km round trip to QLD on Thursday. I'm fairly relieved with the positive information they gave me, and they seem to know exactly what is happening from experience. They were also more than happy to do the flush tomorrow for me. If anything goes wrong, It'll be up for them at warranty again, but I'm confident that what they have told me is correct.