Here are my suggestions:
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Keep the ground and clock wires between the Arduino and the CCD as short as possible. Run these 3 wires right next to each other to minimise the inductance. Even a small amount of inductance will cause ringing, because of the high capacitance of the CCD clock inputs. If you can't keep the length of the wires to a few cm, then use a 74HC04 chip to buffer the signals, as shown on the datasheet (and keep the wiring between the 74HC04 and the CCD as short as possible).
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Make sure you have a 0.1uF decoupling capacitor connected across the CCD power and ground pins, as close to the CCD as possible.
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Switch the clock lines simultaneously using direct port access. To help make sure that they cross above 2.5V, try either:
(a) a 150 ohm pullup resistor on each clock line, connected as close to the CCD as possible; or
(b) the Schottky diode/parallel resistor arrangement I suggested earlier.
- Double check that you are sequencing all the CCD inputs correctly.
What do you have the output of the CCD connected to?