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Bought a 2013 Yz250F, question about rebuild and forks.

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I am a long time reader and finally created an account and bought my first bike, a 2013 Yamaha Yz250F. I come from the street bike world owning and riding all types of bikes. I currently own a Multistrada 1200s and that bike convinced me to get my dirt bike. I am excited to get into a new hobby but I have two questions. The first question is when to change the bottom end? My bike supposedly has 40 hours on it so I will be doing the top end next week and checking the valves. I see all these posts about bikes blowing up and I dont want that to happen. I am the third owner on the bike and the second owner sold it to me because he only put 20 hours on it in 2 years and didn't have enough time to ride it. The bike does need some tlc so I already ordered new cables, grips, levers, filters, and brake hoses. I will refresh the plastics last. Mechanically I am pretty good at tinkering with things and have watched a rebuild of a 2004 Yz250F on YouTube and I feel like I can do it, I even bought the service manual to assist me. I will not be racing the bike and I bought it to explore the land around me (Midwest). I will also give it all it has once in a while to have fun. Let me ask you this, given this info, should I buy the tools and replace the bottom end as well? The second question is I tore down the bike to give it a nice cleaning and found a huge gouge in the upper fork tube. Time to replace the upper tube? I will attach photos at the bottom to show you. 

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Edited by Jason Mikel

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The gouge is from the fork protector rubbing. There is a wear ring on the fork stanchion that prevents this under normal circumstances. Look at the guard and make sure it's mounted correctly. Perhaps the brake line is incorrectly installed and causing the unusual deflection. At this point, I would only classify that as cosmetic damage.

You purchased one of the most reliable 4 stroke engines in motocross. I would definitely inspect the crank for wear while the top end is apart but I expect you'll find it is still within specification.

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Thank you for your response, I will open her up on Thursday, inspect the crank, get the cylinder honed/measured and order a new top end. Now, the fork is developing a small hole where the fork protector is rubbing. Should I clean it out and epoxy it? I also saw a few KYB fork uppers on Ebay for $100 and under, could I just replace the upper and call it a day? They don't have the same wear ring design though.

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I did notice a bit of oil on the bottom tube which I think is due to a leaking seal but not a major amount of oil, that was before my first ride. I came back from my first ride, washed her and tore her apart in the garage in preparation of my parts arriving. I should of noticed oil gushing everywhere from the hole right? I'm hoping this is something I can fix but if I need a new upper tube that kind of sucks. The fork protector is rubbing on the fork btw, the brake line is nowhere near rubbing. 

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I highly doubt the bottom end would need replacement, unless maybe it was extremely abused.

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I always like to make sure my toys are in tip top shape before I take them out to play. I will open her up tomorrow, check everything and report back. Hopefully all I need is a top end and fork seals. 

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