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I have a dynojet quickshifter on my 03 1000 and I have noticed a few times that it will slip out of second gear down into neutral sometimes. I am not sure if it's a function of me not pushing it into second hard enough (which I am definitely guilty of sometimes) or if it's actually slipping.
 

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Here is my 2 cents. My 2nd gear wore out on my 2001 gixer 600. It never went into neutral but just slipped under a lot of power at first then later with just a little bit of throttle. I got another transmission off Ebay and installed the two gear shafts. After looking at the gears, I realized they are designed such that the they pull into each other (engage more) under hard acceleration. However, this portion of the design in my 2nd gear wore out. So, I don't think it would slip out into neutral if the 2nd gear is physically worn out. Since you have to go through neutral to get to second, the quickshifter probably isn't fully making that jump.

Does it still slip to neutral after DOWNSHIFTING into 2nd?
 

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Disconnect the quickshifter from the shift linkage entirely. Then ride the bike for a bit and see if it pops out of gear.
If it pops out of gear,without the QS attached,you have worn dogs on the gear,your shift fork is worn,or both. It'll be time to split the cases and either have the gears undercut,or replace gears/drum/shift forks.
 

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Disconnect the quickshifter from the shift linkage entirely. Then ride the bike for a bit and see if it pops out of gear.
If it pops out of gear,without the QS attached,you have worn dogs on the gear,your shift fork is worn,or both. It'll be time to split the cases and either have the gears undercut,or replace gears/drum/shift forks.
Solid advice!!

Just get you a tranny off of Ebay from a K5 or newer model. Everything will interchange.

Just keep your 1st gear and 6th gears from your K3. 1st gear is lower and 6th gears is high than the newer models. Gears 3-5 are closer ratio and slightly lower for better acceleration.

Throw some Ceramic tranny bearing in too. It will shift so smooth!!
 
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