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At the end of my Rope - '01 YZ125 Stuttering/Jerking Issue

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Notes on bike:

2001 YZ125 

1.3 hours on fresh rebuild

Wiseco crank, all new bearings, seals, 

Wiseco piston

Head coated at Millenium

stock bore and stroke

carb rebuild with all new gaskets, set to factory spec, new jets/needs also factory spec. 

47:1 mix, red line synthetic, 93 oct

stock exhaust, fresh oil air filter. 

 

Problem:

 

In second gear, at any throttle input the bike jerks hard. Like something is cutting gas or spark randomly causing it to buck. Doesnt matter if I am putting along at 2k rpm or holding it wide open. It works perfectly in every other gear, in every other speed. Put it up on the stand with the rear wheel up, and dropped it into second it runs fine. But with a person on it, it jerks hard. 

 

ONLY IN SECOND GEAR.

 

What the &%$#@! is this? I have tried everything i can think off. 

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The only thing i could see is the second gear in the tranny is beat

That's one possiblity. You can drop the oil through a pantyhose and see if you collect some shavings. However, usually if one gear goes bad, it'll take another one with it...

What about the CDI? Can you swap it out with another unit?

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Nothing handy. Talked to a local shop guy i trust and he said its the second gear popping out. Shit. 

sounds plausible. Its one of the more common shift forks/gears that go.

Does it make some pretty gnarly clunking sounds when it happens?

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