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Hi Peter. If you can get hold of it, Aip4Win has an interesting section on Testing CCDs. Part of the process is the construction of a 'regulated' flats box that doesn't rely on shooting through your scope. If you are interested, I have a box i've made that I can bring to Astrofest, if you are interested in refining your readings.
As for exposure times for flats, the way it was explained to me exposures of between 2 and 10 sec produce the most reliable flats for any given situation. I try for around 6 sec and also do flat darks.
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