Ok, before someone gets mad at me for resurrecting an old thread, this diagnosis information is valuable and still very valid.
I have a 1995 Polaris Magnum 425 4X4 and I am having the EXACT same problem.
Did you ever figure out the problem and if so, what was it?
My carb has been rebuilt, new fuel pump, new fuel lines, new OEM Polaris air filter, new OEM fuel filter, new recommended spark plug, fresh ethanol free gas.
With airbox cover on it bogs down, with airbox cover off it runs way better but will not go over 40 mph, but at full throttle with the cover off I get that more powerful high rpm sound you get when you goose it. with cover on it bogs and struggles.
It seems like something is restricting airflow but it is not.
Could the carb just be needing to be adjusted to allow more air?
When it is warm with airbox cover off it and in neutral when I rev it the engine quickly returns to idle like it should if it the carb is tuned. But maybe there is room there for better tuning?
Any help would be appreciated.
Jeff