Don't know about the yam but i had a full stage 3 tune on a suzuki 600.
Cams, vernier gears, filter with a full 4 to 2 to 1 race pipe (not a 4 into1 thats nasty) with the limiter lifred and a full dynojet kit.
The dynojet had different jets for the carbs depending on it being an inner or outer cyl.
That had 32 dyno runs all told to get right all done by TTS.(SUPERB PEOPLE)
Below 5 was a waste of time from 5 it was smooth as glass and from 8 it fked off like it was shot from a cannon.
I would stay over 2k rpm. Why are you riding it that low anyway? Its doing the bike no good at all.