Brett,
just a thought but have you considered doing exactly what you proposed - except - switch the bypass to open instantly in response to the SC OFF conditions mentioned. Then put your 1-2 second delay on the SC clutch.
Would help turbo transition a bit i think. Would also help to stop the SC contributing to the pressure waves that'll be bouncing up and down your intake on gear shifts, but still keeping it on. Maybe add a BOV plumbed back into the bypass...
Bookmarks