Thanks for posting those, interesting to see the setup.
The flat flexible connectors are very vulnerable to tearing and it will be impossible to prevent dust getting on the CCD cover-glass.
At least, with astronomical images you will not notice the dust as much.
I can only assume that the sensor read-out time is somewhat longer than the above shutter speeds.
As the sensor is still exposed to light during that time, the set exposure will have little effect.
To clean the sensor, very carefully wipe with lint-free tissue wrapped around a cotton bud and wetted with window cleaning fluid (such as Windolene).
Then with fresh dry tissue, breath on the sensor cover-glass and carefully polish.
I would ask again, why are you not using the usual afocal method with an unmodified camera ?
Here is an example :-http://stereo.jpn.org/eng/sdm/digi.htm
By removing the lens you have not turned your camera into a digital SLR