Motorcycle Repair: 2nd gear slip on 02 yamah R6, yamaha r6, yamah


Question
I have a 2002 Yamaha R6 with about 15k miles on it, got it from an auction. The bike must have slid on the right side causing mostly cosmetic damage.  The only bothersome problem is with the 2nd gear.  It jerks when accelarating only in the 2nd gear, all other gears are flawless.  Its not noticable when accelaraing at a very slow rate (granny style), but jerks when at medium and hard accelaration. (the harder acceleration, the harder/bigger the jerk) Apperantly its a design/factory defect, an R6 weakness. I'm considering doing the job my self, but i'm just wondering  if i can correct this just by replacing the 2nd gear or pinion or something to do with the second gear(once i open up the trans). I'm not a mechanic, but can "replace" pretty much anything on a car or bike (never worked on internal parts of a transmissions or an engine tho), so am wondering if i will need special tools or machines to check/correct specs or if this is just a take of old and install new part operation. :) I'm looking for r6 manual but will be using sites like  bikebandit for parts and blowup parts breakdown. If you have any suggestions as to how go about this, anything greatly appriciated. thanks,


Answer
From your description... check the chain and sprockets... are they worn, chain loose, sprockets hooked, etc...?
There is considerable torque in the lower gears, this is where a jumping feeling will occur, especially with a bike with so much power.
If chain and sprockets are great, the jumping issue could be the gear dogs when 2nd gear is engaged... this would be from some serious abuse from the previous owner and the only way to be sure is to open 'er up... What does the oul look like ? Is there metallic stuff in the drained oil ?
My initial thoughts are chain jump and bad chain/sprockets...
P