This schematic might help.
https://www.bikebandit.com/oem-parts/2002-yamaha-yzf600r-yzf600rp/o/m145684#sch255154
SOURCE: Fork seal replacement
Did you try taking down the fork seal and cleaning out with wd/40 and a piece of 30mm film? You should always try this first. The seals rarely go bad. There's probably just a vary small rock holdeing it open and the film will dislodge it the wd is just to help things along.
SOURCE: 2001 YZF 600 R thunder cat: Yamaha yzf 600 Thundercat when under heavy load or...
Many YZF 600's have a problem with second or third gear, under heavy accelleration they will jump in and out of gear, the fix is in the gear selectors,an internal box problem.
If it is a clutch problem, ride in top gear at 100kl\hr and give the clutch lever a flick, see if it grabs or slips for a while and then takes up.
SOURCE: Lost key for 2001 yamaha yzf 600 r thundercat, I
The site below has diagrams of the bike in exploded view form...Electrical #2 shows the steering lock also. Cheers.
http://www.boats.net/parts/search/Yamaha/Motorcycle/2001/YZF600RNC%20-%20YZF600RNC%20%28CA%20Ed.%29/parts.html
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