Definatley make sure you put the piston in the right direction, Like Toby said the arrow on the piston needs to be facing down towards the exhaust.
Did this problem exist before rebuild? I'm guessing it did that's probably why you rebuilt it.
The rear spring has very little impact on the shifting, the shifting is mainly controlled by the weights and variator, (Front part of clutch, weights are inside the variator)
To me it sounds more like carburation, could be air screw setting like previously stated or to large or to small of a pilot jet. Pull the spark plug and see if it is really black or really white.
Is this machine all stock?
Kevin Smitley
Brandon Smitley #423
B.A.K. Motorsports
2005 TRX450R Race Bike
2006 TRX450R Practice Bike
Special Thanks to:
Dave Carter (DC motorsports)
Bruno At Quadified Racing Engines
Fly Racing / Western Powersports
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Impact Solutions
Elka
Leatt
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All Balls Racing
Slick
Grandma and Pappy