I have a buddy that has a Polaris 700 with the Liberty engine. (2000 or 2002 I believe) It bogs off the line and sometimes stalls. Top end is great, (if you can get it there). It burns a ton of gas too.
We rebuilt both carbs and replaced the reeds. New fuel filter and swapped fuel pumps with another machine. Also tried re-jetting the carbs several times. Same issue.
I had a similar issue with my CAT, it was the throttle position sensors. I do not know if Polaris has them. I just unplugged them and all was fine. I did the dame thing of taking the carbs apart....
I had a issue with my Polaris 500 that kinda sounds the same. From a standing start if you would hit the throttle wide open right after you started the engine it was fine but if the engine would be warm it would bog down or stall out. I could play with the throttle giving it just a little bit of gas to slowly get up to about 40 mph and over that it was fine. I ended up taking it to a place to have it looked at and the PTO side oil jet clogged which eventually burned up that piston.
Could have a bad crankcase seal.
Might check for cracked carb boots also.
Or, does it seem like the clutch is sticking(not engageing/ disengageing properly)?