Quick and dirty thing I wrote about motor building. I need to expand it more in the porting and cam profile area.
Building a motor takes forethought and planning, different parts can't be thrown together and expected to work 100%. First off, what are you building it for? What's your budget? How and where do you ride?
First choice is the piston, the popular choices are wiseco and JE. This is where you decide what bore and compression you would like to be at. If you're looking to go mild then a wiseco 10.25-1 is a good choice or the 85mm 10.5-1 JE. If wanting to build a performance motor then look into the 12-1 JE. If the higher compression piston is chosen then at least a half mix of race gas is recommended. The higher your compression, the more you will feel a boost in the lower rpm as the increase in cylinder pressure is what helps get the quad up and moving.
Is a port and polish in your budget? A good port will increase flow drastically and will help your motor inhale and exhale. I personally recommend using someone with experience, the proper tools and possibly even numbers to match them up.
Next is cams. Did you decide on that port and polish? If not I would look into a cam with a smaller lift as the stock head peaks at .400" of lift. Good cam choices are the hotcam stage 1 and 2 or the web .390. Maybe even the web .413 or mega .415. If you went with a port then I would look into a cam with a larger lift such as the web .413 or mega .415 again or the web .430, web .440 or the mega .450 as the higher the lift will equate to greater flow. Now to match cams with your piston. The larger cams like the web .430, .440 and mega .450 have a higher duration. The higher your duration the longer you can keep that valve way open giving big top end gains but on the downside the more compression bleed off you will have, or a lower "dynamic compression". Now the higher your compression is, the more you feel the power come in the lower rpms. If using a high compression piston, one of the larger cams with greater duration can easily be used as you're starting with a lot of "static compression" giving you sufficient "dynamic compression" even after the slight bleed off. If running one of the lower compression pistons, I would recommend one of the cams with less duration like the web .413 or mega .415. If looking for top end on one of these lower compression pistons, the web .430 or mega .450 cams are recommended as the web .440 just has too much duration with will drop your dynamic compression too low.
The difference in cams are the lower end the hc 1, hc 2 and web .390. The duration increases repectivly in them giving the hc1 the best in low end and the web the best mid to top. The mid cams, the web .413 and mega .415 are good for giving decent gains in power yet having the low rpm torque. The web .413 actually has less duration than the web .390 making a great "torque" cam, the mega will be the better of the 2 in the mid department. The web .430 is a great mid to top end cam, while the mega .450 and web .440 are the top end grinds with the web actually having the most duration. My speculation for the most efficient cam for this motor is a higher lift, shorter duration cam. If a custom grind was to be made I would do a lift somewhere at .430 with the duration somewhere between the web .413 and mega .415.