I use the same graduates for everything - E6, C41, B&W neg and reversal, everything, just as I do all the tanks, and Lomo spirals, trays, etc. I use regular tap water, never distilled. Maybe I've been lucky, but I've not ever suffered any cross contamination nor development issues that I thought warranted separate equipment for each process, or the use of distilled water. In terms of contamination, I just rinse all out well - not excessively, just a good rinse, and I'm onto the next, so I don't know... unless people don't rinse their stuff out, I don't see how cross contamination is this much of an issue that you need equipment duplication. If it gives extra piece of mind, cool.
My advice would be to maybe watch temps more closely, especially on such a temp dependent process. That is the one thing I am really careful of, although it would seem as if you should have gotten better results regardless.
Arista's E6 kit has "rapid" in the name. That could be why the shorter color developer time. On my directions, it says 4.5 min for this step at 105 deg.