What is the size difference between the enclosure they were co-habitated in and the smaller ones you plan to separate them into? Could it be the smaller quarters that are agitating them? Or, perhaps they just need some settling in time. I often heard it suggested to treat cage moves the same as a new arrival: no handling or feeding for about a week.
Also, not sure if they'd still be wanting to breed this time of year, but that could possibly be the reason for the nose rubbing and not necessarily stress due to separation. I've often read that snakes will cruise or rub when wanting to mate. Placing them in separate enclosures and separate rooms is probably the best and really only suggestion to put you and the snakes at ease.
I have also read and been told that females are more likely to ovulate if kept in the vicinity of males, so keeping them in different areas of the house may not be a bad idea long-term.
Just give them time and don't over-analyze and worry yourself to death. They could be sensing your stress and that's what's stressing them out
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