Non of the Honda's were that good, so even if Rossi's bike was in actual fact a re painted Factory bike that wasn't saying much.
check out the championship standing for that year
My link
Basically hrc/criville screwed the bike up without doohan and it took rossi etc half the season to fix it as has been said. I am well aware of how the championship went; garry mccoy won a race on a privateer yamaha, and valentino scored a lot of points in the second half of the season. Despite this, honda managed to conclude that their almost unbroken run of success up until 2003 was due to their engineering prowess with rossi and doohan apparently only playing minor roles.