None of this is really about braking power, it is about having more thermal overhead. Unless you are tracking your bike going to other calipers or larger rotors is simply not necessary - the brakes are sufficient to lock up the tire so there is more stopping force available than traction...
The issue seems to be that the stock rotors eventually warp/get hard spots due to metallurgy. Nothing other than different rotors fixes that. I've never had an issue with how hard the bike stops and adding the larger rotors and brembo pads only made the braking better.
I just happened to look as I was chucking up a piece of 20mm aluminum bar stock in the lathe to make my own. The bar stock would have cost almost as much as I paid for them from Amazon.
I did not and I didn't see your comment until it was too late to add to that order. $50 from italy for a pair vs $120 in the US. But I saved so much on the rotors I didn't care and just ordered them from amazon.
Holy hell!!
Edit: Just ordered the Brembo rotors. I like the look of the Galfer better but if it is metallurgy that is causing the warping issue I don't want to find out that the larger rotors will wind up with the same problem, I'm just now starting to feel pulsing right before I stop.
Rottweiler has a front wheel 320 kit for our bikes using Galfer wave rotors, going to try that. The best I can find the Brembo 320's are on on the order of $400 each...
https://shop.rottweilerperformance.com/oversized-320mm-front-rotor-kit-790-890-990-duke/
First thing I do on every bike is switch to a Shorai. 6 pounds of savings up high on the bike. The one in my MT09 is six years old and still cranking faster than a lead acid.
All of the issues you are describing will be taken care of by a FuelX. All it does is slightly richen the mixture by adjusting what the O2 sensor reports. If you do a full exhaust or a decat you have to use a Coober or other such thing, but on a stock bike the Coober is a waste.
If you went from the stock muffler with baffle to the Remus with a baffle I find it incredibly hard to believe that is your issue, the airflow just can't be that different. People have totally removed the baffle from the stock can and not had issues, that would affect flow way more than another...