Back in '06 the dealer could download a digital tech map to the ECM WITHOUT having to have a tuner like the SERT. The cost was about $150 and was commonly done to bikes that had the mufflers swapped out and a change to a high flow air cleaner system like the SE backplate and K&N filter setup. I'm assuming you have the OEM air cleaner setup? If it's a relatively closed "box" with an oblong filter in it, it's stock. If it's a round filter and you can see all around the filter medium, it's not stock. The combinations of downloads available in '06 was limited. I had the old SE "b" style mufflers on mine with the SE A/C setup and got the download before I ever picked the bike up. It ran fine. I later did some changes and had a PCIII added with a tune and the bike never pinged...but, I had the original 5 speed. However, RPM is RPM, regardless of how it gets there...a bike that runs fine with a 5 speed at 2500 RPM should also run fine with a 6 speed at 2500 RPM. The RATE at which it accelerated up to 3000 RPM would be different, but nothing else.
Some owners stick parts on their bikes, or the dealer does, and they think "everything will be fine". That is rarely the case. Regardless, your bike should not ping...ever...if tuned properly for normal riding.