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Join Date: Jan 2011
Location: Smack in the middle of Illinois
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Cap nuts are used prevent oil from running down around the stud and causing a leak at the head gasket for the 3 inside the head cover and preventing water from penetrating the threads and causing corrosion on the one stud outside the head cover
It's not of great concern if you are not worried about an oil leak - personally; I am rebuilding 2002 400EX - I am installing all new washers and cap nuts on the head as 2 are distorted and one is punctured from being installed either without washers or wrong thickness washers or from someone re-using gaskets or over torquing or a combination of more than one possibility.
As to the length - specified length above the gasket surface of the cylinder is; 81.5 mm for the on on the exhaust side, 62.5 on the intake side and 49.5 on the left and right sides - the one i'm working on measures 81, 62 and 50 (measured with a tape measure)