Glad you've seen an improvement, Steve, and you can't fault Neil's customer service can you?
Your situation mirrors my own, in that you're coming from a custom-mapped S2R to a stock Evo. And your observations following the remap reflect my experience too.
Lowering the gearing will improve matters further and also make sixth gear useable, rather than the virtual 'overdrive' it is on stock sprockets.
Also don't forget that the S2R is twin spark and its flywheel is twice the weight of the Evo's; both factors that will allow the S2R to run better at low, steady, speeds than the Evo.
You may well find that it improves further over the next couple of hundred miles as the ECU relearns the autoadaptive parameters.
Enjoy your 'new' Evo!