The stock header is the big downfall of the exhaust.
I have made new mids for my first gen and ran it on the dyno with stock mufflers and mids then with the new mids and GSXR1000 mufflers and it was the same peak HP but the GSXR mufflers gave me a boost in the middle of the range.
Big steve ran his bike with stock mufflers and mids then stock mids and aftermarket slip ons and with the aftermarket slip ons on the new mids and he came up with the stock mufflers and new mids was the same as the aftermarket mufflers and new mids.
We came up with the thinking that the stock header is what is chocking it down.
Ill post pictures soon.