2 speed blower? What blower are you using? What engine RPM are you running at? The reason I ask is that when selected to the 540 RPM position, you only get the 540 RPM at the PTO shaft output when the engine RPM is running at it's max governed RPM(full throttle), probably around 2200-2300 RPM on your tractor's tach. This area should be marked in green on the tachometer indicating the proper area to get the rated RPM on the PTO shaft.
My experience with PTO impliments is limited, but I have never run across one rated for 1000 RPM on the PTO shaft. They have always been 540 RPM inputs. If you are running the engine at less than max rated engine RPM(say around 1200-1500 RPM), then selecting the 1000 RPM PTO position would yield a PTO RPM in the vicinity of 540 RPM. Have you tried running the tractor at full throttle, PTO selector on 540 and moveing slowly in creeper gear?
My experience with snowblowers is all walk-behind, but with wet snow, you need to keep the snow flowing fast thru the chute, and too much snow input slows things down. If it cloggs, I either have to slow the input speed(slow down my travel speed) or take less than a full width pass to lower the snow intake and give the blower time to process the slush/slop.