I'd start by checking the spark plugs; they'll tell whether you're running rich, lean, or spot on.
My '87 Phazer was bogging a bit on the top end (would top out at only 75 with the track off the ground and no load on it), turns out the carbs weren't tuned properly for the high altitudes I ride at. I had to drop down in size on the main jets and move one of the rubber circuit plugs over the pilot jet hole and it
really woke the motor up. The thing was screaming on the top end but probably needed a bit more fine tuning as the plugs were still looking a bit lean, but unfortunately I had a bit of a wreck. More info about that in my thread here:
http://www.snowmobileforum.com/yamaha-snowmobiles/55464-90-phazer-ll-excessive-smoking-wont.html
Are you riding at a different altitude than you used to? Seems to me like these sleds are really sensitive to altitude/temperature changes, and if the carbs aren't jetted/tuned properly they won't run right. The free manual available here (note that the manual actually covers '84-'99 model years, not '84-'89-that is a typo):
http://www.snowmobileforum.com/yamaha-snowmobiles/39584-1984-1989-yamaha-phazer-manual-pdf.html has a jetting chart. It is indispensable when tuning the carbs.
As suggested previously, dirty carbs can hinder performance as well. Gas can go bad in only a few months and clog jets, circuits, etc. Is the fuel fresh? You may also want to check the fuel filter, and even the fuel pump (although I doubt that it's the problem).
If it's not a fuel issue, then start troubleshooting the clutches.
