Kcander.. welcome to the forum, officially!
You are asking the same questions that nearly every bueller has asked and pondered throughout their ownership at one time or another.. my response, albeit "knee jerk" is this.. you can play around for "effect and experience" with different combinations of exhausts, intake, ecm programming etc etc to reach your desired goal.. however, if an immediate rideability improvement is desired and your ultimate goal, there exists a higher level of refinement available today in the form of an "over the counter" EBR ecm custom tuned to the exhaust and intake combo of your choice.. there are a number of excellent exhausts produced here in the usa and overseas, check which exhausts the EBR ecm supports, if that is the path you choose.. this "should" be your first purchase decision. Expect to spend a grand or more for the whole package. There is another route to take with an ECM tuning school by "Max" at the "tuniversity" he offers different levels of instruction to teach YOU to custom tune your ECM to your "specific" bike and modifications, (or with "your" datalogging, he will do the work for you..) This is arguably the the best path to rideability perfection, and knowledge of the inner-workings of fuel management. The up and growing "Twin Motorcycles" also offer ECM + exhaust combinations which are plug and play.. they are based in the Netherlands, but now have an aspiring outlet in Texas, so the dreaded shipping expenses should be coming down now & in the near future.
Best of luck with your choice!