Yz426f head gasket issue

Had to do a base gasket so I tore the top half of the motor apart. Got everything back together and it's leaking from the head gasket now. Used new cometic gaskets for everything. Perfectly tourqed down. Took it back apart and noticed a few things on the new head gasket. Looks like it's peeling and a few of the holes don't line up good. Would that be my issue or warped head?

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I would try a different gasket kit or get oem . I would not use a gasket that partially blocks water ports. I would think that would definitely be a leak point.

The head gasket is likely designed intentionally to partially block certain coolant ports so that coolant has to flow over the largest possible portion of the head instead of bypassing parts of it.  It's commonly done on most all engines.

 

That said, I use only genuine Yamaha gaskets for critical applications like the head.  As to whether your head is flat or not, remove the studs and check it with a straight edge or run it over a sheet of sandpaper on a known flat surface.  Check the cylinder too.

It's just odd that the previous gasket that wasn't leaking the ports lined up perfectly with the head. I work in a quality lab for automotive so I'm going to take a dial indicator to the top of the head and check it that way.

On the first picture it was leaking directly in front of that misalignment. That's where the previous gasket fit perfectly. I would've thought cometic would put more time into their gaskets.

The port that is covered by that area is, as I recall, a long curved oval that extends from the slightly misaligned round hole to the far end of the slot to the left of it.  This is what I mean by a deliberately restricted port.  In your pictures the front of the head is to the left.  The coolant from the water pump enters the cylinder at the front of the base gasket and rises through the head to the radiators.  The port restriction is done to force the bulk of the coolant to flow up and and around to the rear of the cylinder, then up and over the head mostly from the rear to the front, where the outlet is. 

 

The small round holes are steam holes.  These prevent the formation of steam pockets by letting letting it out at the high points of various cavities.  As long as they are open enough to do that, they're nothing to worry about, and they won't have caused the leakage.

Wow thank you for your detailed reply that helps me understand the actual flow of the coolant. Under closer look at the actual head it seems there are two small scratches right where it was leaking. I have attached a picture to give you a better look. Could the coolant even make it that far past the gasket? Probably a thousandth or two deep.

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