I'm not sure where the picture count is stored, but the folder settings and prefix strings are in HKCU\Software\HTC\CameraWizard(PocketPC)\3.00\.
The individual mode settings are in HKLM\Software\HTC\Camera\P1 etc that will let you change the folder, format and a couple others.
HKLM\Software\HTC\Camera\Captparam has a setting "EnableDateFolder" to store each day's pictures in a separate folder.
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