I am a military pilot with over 6 yrs. of active service and have been in CAP for one year. Does my military pilot time count toward the time requirements in CAP 35-6 which requires that a CAP Senior Pilot Rating have been an active CAP pilot for at least 3 years?

Yes, there are provisions to apply for a waiver to substitute military-rated service for the senior and command pilot CAP service requirements in Paragraph 7 of CAPR 35-6.