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.
 
The "tune you did was just a light map adjustment to the idle air speed and a general shift for emissions. Nothing to do with actual fuel mapping for more power. Unless internal mods are done... Not much power is gained for any modification well at least nothing that your but Dyno can tell the difference from other than being more peppy and loud. Just saying.
Did you pull out the secondary idle butterfly valves?
You can also check the sweep of the tps with tune ecu.
If no then I'd say you were running rich before and now it's a bit closer to correct. Most bikes including the rocket does not just go with out some throttle from a stop with out stalling.
I would say you should also not be in that habit in riding. Lean how to work the clutch slip zone and not move the throttle past 1200 rpms.
I'm fairly confident that you have no issues and to solve what you want done is to upload the old tune and put it back to stock. But imo it was probably running too rich at idle as it was.
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.
 
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