Okay, my 02 runs HEL lines, EBC HH pads front and Honda stock pad rear, stock forks and shock, and I can stop on a dime and have great feel. My master cylinders and calipers have 50,000 miles on them, and I haven't rebuilt them. Given that the bike only had 20,000 miles on it when I got it, I suspect they have never been rebuilt.
I'm smelling some sort of hydraulic problem, and given everything you have done, I would bleed the brakes, again. I have no idea of your skill set, but I passed on installing new lines (as you probably know, there are 9 including the clutch), and handed it off to a private shop because I suspected I would never get the lines bled correctly.