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04` CRF 250R piston ending the stroke too high?

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So i recently rebuilt my crf top to bottom, and used an 06 crank instead of the 04 now the parts numbers matched from 04-09 so i didnt think much of it upon rebuilding and having a few AWESOME rides(it ran better then it ever did) i had a knock one day in the woops, shut it down to avoid any damages got it home tore it down, to find out the valves were out of spec, No problem got them back into spec then i drove it after it was shimmed ran great no noise, awesome right. me and my friend were racing eachother(on the road, a... empty.... pedestrian free road that is. (: ) and it came back the same knock, it never made a difference in the bike running so being as i was so far from home i putted back, and upon tearing it down (once again) i found that the exhast edge and intake edge of the piston were rubbing the head, And noticed the piston went wayyy further then the stroke should allow it, at top dead center the piston is even with the cylinder head(not submerged like it once was) now im either thinking my gasket is not thick enough or my rod stretched. Any takers on my issue ? 

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Check the base gasket between crankcase and cylinder. If you omitted it or used a thin aftermarket gasket, or used gasket maker instead, you would have reduced the head clearance, probably not enough to touch normally, but....

If in addition, the bore is too loose for some reason, the piston might rock up and kiss the head, especially with the added compression and knocking.

Let me guess, you bought used parts on ebay?

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Right on the money mudguy. i knowingly purchased a used crank, and tusk gaskets from rocky mountain. I got bent over for 200 buying prepaid visa`s(clerk never swiped to validate the card) and had to resort to the dreadful hell hole known as ebay. 

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The tusk base gasket is ok, I would not run the tusk head gasket.

Exactly what parts did you replace with used parts? Maybe someone shaved down your cylinder or head.

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I just hate that about this bike so much, when its working it works at at a top, like A++ torque monster fastest 250 around my area, and then BAM! layed up. And I know all about the head gaskets by tusk, I wish they would fix that issue, there such good products. I had it blow on 3 of my bikes. But this one is holding up, i have the base gasket on order be in wedsnday and have a head gasket, Just have to pick them up, Hopefully they solve my issues.

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I don't think that will solve your issues, the tusk base gasket is close enough, the head gasket is inferior quality and prone to leaking but is comparable height to the honda gasket.

 

If you take good pictures of the piston in cylinder at TDC, of the bottom surface of the head, and of the piston and all sides of the cylinder, i'm sure one of the engine builders around here will be able to figure out what is wrong.

 

Also check how much piston rock you have, rock it front to back and see if it is exceptionally loose. Should be fairly tight.

 

I was actually thinking, are all of your rings in place? If you were missing one of the oil rings, the rocking could be amplified significantly, maybe allowing the piston to kiss the head.

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I find it odd that one min its ok and then its not.

Valves out of spec would not cause that.

From 1k miles away I'd say your lower rod bearing is cooked. Or you got a stroked crank. 

Where'd your crank come from?

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