A little lost here, hard to understand (unless one's experience ist based on KTMs) what the uproar is. You shouldn't need a new piston until at least 50000mls = 80000km.
Unless that shop is more than a little versed in big bore singles, I am not awfully sure what they are measuring. Of course, they can confer with the shop manual. So can you and you should download the official Yamaha SZR manual (Same engine and thus same data for all important questions). Or get a XTZ handbook.
Same goes for the head. Yamaha valves and guides are good for at least 100000km (not a typo). You can clean out the carbon deposites if you want. With proper usage, there should not be much at all.
Re: deco, it is really very simple, so simple the manual need not go into it. Just put it back together as it was. Inside the cam, there is a slender secondary cam with actuates the small plunger in the lob of the left exhaust valve.
This is the hole for it.This cam has been modified for use without the deco. The weights on the cam sprocket turn that slender shaft as RPM pick up, just like an oldfashioned distributor. At rest and up to about 600RPM the plunger protrudes, thus not allowing the exhaust valve to close, above the ±700RPM the weights swing out, turning the shaft and allowing the plunger to retract and the valve to close. It is that simple. No voodoo, no gimmick mechanics like on the XT, SR and SRX to couple the deco to the kickstarter, no hand trigger and no need for it. Drawbacks? For a civilized street engine few. It can break and has. You cannot check the compression. Given that the engine is nearly indestructible, no need to for a street engine, either. For more extensive tuning, tho, it is a good idea to remove it and some racing cams have no provision for it.
So, that ain't no marks for it, cause there ain't nothin to set. You can only bolt on the timing gear two ways, the right way and - 180º off - the wrong way. There is nothing in between. Use a GOOD torque wrench for the those M7 bolts and be careful of them.
The 3YF is the next best thing to a an old John Deere. It is not a Ferrari. Leave it alone until it makes itself known.
One thing you ought to do, tho, when you have it apart, is to replace the gear for the balancershaft.
You'll find losts on the subject in the archives and some here in my blog:
http://cembalobill.blogspot.com/2010/03/update-sp-2010.htmlYamaha parts number for that gear: balancer gear Raptor: 1S31153600