Something changed

If I'm understanding correctly you bought the bike with TORs and it ran fine until you installed the Ram Air. Suggestions for another tune might help. When I had my '11 Roadster with TORs and K&Ns I ran Martin-Brighton-uk 's tune (search for it) and it ran great.

BUT, wondering if it could be something else like cracked vacuum hoses or caps on the throttle bodies (should all be new now, I would think), TPS failing, and or the small wires going to the coils need to be cleaned and crimped to fit tight. Let us know what you find out.
 
No I haven't pulled the secondary. Everything stock. I have TUNEECU but haven't played with it because I have no experience with tuning.