Clean and clean some more, but something that people often over look while cleaning the work area is the area where you will be laying out your negatives to cut and sleeve them, and where they will set them before doing whatever it is they want to do with them to print them. Clean your printing mechanism all you want, it will make little difference if you set your negative in dust while you are getting ready to print it. Also right before laying your negative down to make the print, dust it and the paper.
I have several microfiber towels that I use, then toss in the laundry. I have never had a scratch from the dust remaining trapped in them. I use one for the work area, another for the negatives, one for the paper to be printed onto (I do cyanotypes), and two for the glass, one for the first cleaning of the set, and the other every time I change the negative. This works for me, your actual mileage may vary. Please note, microfiber towels are dust magnets, and must be cleaned often even with that they will, not might will scratch something during a print session.
No you can not clean too often during the contact printing process.