I don't disagree about a freer breathing exhaust and some extra kick in the butt hp, but the glowing header pipes and the detonation or pinging, is most likely caused by meeting emissions and how lean the ECM is set up to meet these standards.
If you run freer breathing exhaust it will cause an even worse lean condition. The same for a freer breathing air cleaner. Lets look at it this way, you exhaust more air and draw in more air but you program in no more fuel. It has to go leaner and that's just compounding your issues.
That doesn't mean you won't see improvements, you will, but there's a possibility because the motor will be running even hotter that the motor could be damaged without re-mapping the ECM for a richer running injection system.
Sorry I'm going to reference Harleys again, but a Stage I setup for a Harley usually includes exhaust, air cleaner and a tuner for the ECM. Stage II would be cams, compression or head work. Stage III would be all of the above with larger stroke and bore etc.
But the new Harleys run soooooo hot that they had issues with the exhaust valve guide on the rear cylinder on touring bike coming loose because of aluminum head expansion and guide going loose. Their fix was to put a snap ring on the guide to keep if from falling into the exhaust port causing the valve to stay open.
I'm sure that someone has been able to re-map the S&S controller and that should be the first modification. I would guess the guy from the factory running his M3W has done some major tweaks to his ECM to allow it such performance with all of his modifications etc.
Again, this is only my opinion and living through it with new Harleys, it makes a BIG difference in the motor temp and the detonation is gone as well.
I do like what Garage56 has done and it will be a nice addition as a Stage I upgrade, but don't forget the ECM and getting it to run richer.
