I think you're the 5th owner of the bike, I was the 3rd owner and had it from 2001-2008. Not sure if the 4th owner did anything. This was a Japanese market bike and was imported by the 2nd owner, who also did a bunch of mods, such as the race SAPC (I think it was the 23D10), open air box, different gearing, pipes and aftermarket rear tail. He was basically trying to emulate the Suzuki "Hop Up" manual. Have you read it, if not let me know and I can send you a copy.
I never rode that bike much, so I never sorted it out as I should have, but I didn't have a flat spot. I think the open air box, with a race SAPC dulled street performance, especially compared to my stock 95 RS250. Bogging issues might be SAPC/air box related, as the solenoids open at different rates with the race SAPC.
I don't think I changed the reeds, that could also cause bogging.
As for the colors, not sure, from my understanding the bike was pure stock when it was imported. I want to say the 2 different colors was normal.