We picked up huge gains on a 2012 recently done before the race season. Testing/tuning methodology was the same as yours - nothing crazy used, simply the WRT software tuning per cylinder, dyno and lots of time to create individual maps for each cylinder.
From his last tune (combined AFR across all four) it put down a typical and respectable 184-185 to the wheel. After observing, tinkering and finally getting down to business tuning per cylinder, he picked up 10 extra horses putting him in the mid 190s. All on pump gas mind you. We then did another tune for him, this time on race gas and yeah, bike is a monster. We had great results doing this on a ZX-6R as well.
Tuning per cylinder is something that is often overlooked because of the cost since we have to make pretty much four complete maps for each individual cylinder. But for race purposes where the difference between standing on the podium and off of it are a fraction of a second and any advantage you can get makes it worth the extra cost. Good job.