First try loosing the pedals and shoot striate into the amp (nice cables help). Then try setting all your controls to 12 O'clock (Not the volume and gain obviously !). Then try tweaking your mids, volume and gain to get a tone you are happy with.

Then add back the cry baby and the CS-3. Try to keep using lots of attack and a little "sustain" or compression as possible. If possible try to use the channel switcher on the amp rather than the stomp box, which may be were dome of your problems live !