The bung depth and location plays a major roll tuning the ECM in the lower rev range. The bike could be getting wrong data from the sensor not being in the exhaust flow. 12 discs closed cap on a 2-1 pipe is restrictive but ok if he has 2-2 with dual mufflers. If the bike lost throttle reponse after 40 K's I would check the bung depth and make sure it's well in the exhaust flow. The caned maps run great but the first Vtune make a big difference with throttle reponse.
Where are the bungs mounted in the exhaust and do they sit in the exhaust flow with at least 75% of the sensor. If you pull the sensors and there covered in black carbon that's the problem. They should be white/ brown like a spark plug

Supertrapp have a forum on there site with a few years of questions being asked for most of there pipes. 10 to 12 discs work with the open end cap and 15 to 18 closed cap is what supertrapp recommend depending if there internal or external disc systems. Check out there forum it's worth it for your mates benefit.

Thats good news Cookster. The open end caps would make a big difference to the top end alone but wait to you guys run a few Vtunes through the ECM.

Sounds like its running too rich down low, try re-mapping....

Cookster
Well done on the Vtune mate and I bet your mates grinning now. If he fits pipes ,Air cleaner, Big bore, Flowed heads, or any engine mod with a couple Vtunes he's back on track with a healthy running engine.
Great news