I'm assuming the factory ignition timing is sufficient for the modifications I have even with the fueling dialed in.
I've been studying engine theory a lot lately and I've noticed that when a drastic change to the exhaust system is made, ignition advance needs adjustment as well. The reason is that what most people call "back pressure" (in reality it is the ability of the exhaust system to vacate the cylinder of exhaust gases and allow the phenomenon of "sucking in" fresh mixture because of the momentum of the exhaust gas, during valve overlap) affects the speed of flame spreading during the next fire cycle of the cylinder.
If you take a look at the factory ignition advance maps of the Street Triple and the Street Triple R with Arrow 3:1 you'll see significant differences in advance timing, with the ST having significantly increased values at several areas of the map. And this is according to the theory which says that the stricter exhaust causes more exhaust gas to be left within the cylinder, which impedes the spread of the flame front during the next cycle so more advance is needed to compensate for this reduced flame-spread speed.
So I suspect there are even more gains to be had if this is sorted out as well.