Possible transmission problems or?

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So all this problem and the Techs couldn't recreate the issue?
My thoughts exactly. I wasn't quite sure how they didn't notice this. He did mention 2nd gear was a little rough going in, but other than that normal.

At this point though I could care less what they think. I'm waiting on my warranty company to give me a ring so I can move forward cancelling this god forsaken useless piece of trash.

 
Speedo pickup is in the gearbox of your defunct Gen 1 tranny, the Gen 2 uses the rear abs sensor. I seem to remember you can unscrew the pick-up from the old, and put it in the new. If memory serves, there was a thread about this some years ago, I think someone else put a Gen 2 motor into a Gen 1.

[edit]
One thread as a starting point:
https://www.fjrforum.com/forum/index.php?showtopic=24861

 
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He's not using the case, just the gearshafts. I'm pretty sure that's what he means when he says new transmission.

I just consulted the parts fiche at Yamaha's web site, and it is indeed the gear on the transmission shaft that is different from 2005 (36 teeth) to 2006 (37 teeth.) You want to keep the gear from the old box, because even though the gear on the middle gear shaft is 35 teeth in both gens, it has a different part number, and I feel sure because the teeth are profiled differently.

 
I'm also following your saga. They are being shitty. I would go back to the dealership and have the tech ride passenger so he could observe the behavior ;)

 
I called up there and asked wtf happened to cause my forks to not look so bad but the gears and dogs look like shit.

I got told "I'll call you back in 30 minutes"

Guess who never received a call?

I've decided to never go there again. It's a shame too, because I really liked my salesman the service department is a joke tho.

I have ZERO motorcycle mechanic skills (well did now I'm pretty up there I think ;) ) I with the help of the forum diagnosed and began repairing before these turds will even acknowledge a problem.

 
problem-solving-flowchart.png


I think one of the steps is were the OP is stuck and can't arrive at NO PROBLEM.

 
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