You've been getting smoked by this problem ever since you took both side covers off and found a bad change clutch back in April right...? The bike shifted fine back then according to your posts in that first thread, so most likely you'll have to revisit all of the dis-assembly you did back then and then carefully reassemble the motor/trans according to the FSM. There are many possibilities as to what may be wrong with your trans now, it could be a combination of errors... it could be a part(s) installed upside down or even destroyed... so its unlikely anyone will be able to pinpoint your problem & solution for you. Best way to approach this problem is to tear it all back down completely, unfortunately. Once you have torn it down all the way, then we may be able to help you.