I suspect that you also gained some low and mid range torque even with the normal compression overbore kit.
I say tune it, enjoy it, and if you want a little more gusto down the road, replace the cylinders and pistons with the Wiseco kit and slap on some CR26s.
I think that 44.6 hp at the rear wheel is quite rare for a stock 550; that Dyno might be a little bit optimistic, or that might be a very well put-together engine.