If the valves are worn have the seats properly machined (preferably with carbide tooling) to the correct angles and widths and install new valves.
If you are installing stainless steel valves you can lap them after the machining but if the seats are machined correctly there is no need to do this, and you limit your risk of leaving and abrasive material behind that is difficult to clean up.
If you replace your worn OEM valves with stainless and just lap the seats without machining them the stainless valves are unlikely to ever seal properly and you'll reduce the life of the new valves. Stock Yamaha valves last long enough that the seats are undoubtedly worn out by the time the valves need replacing, and lapping won't cut it (pun intended ) when it comes time to reface the seats.
Even if the seat wear is minimal, lapping the seats won't give you a proper sealing surface for a new valve, and you won't be able to get the seat narrow enough for good airflow. It's a very narrow seat that you need to have machined to bring it back into spec. Valves and seats that don't seal properly bleed off pressure and really kill performance at high rpm , and seats that are too wide really hurt airflow which can cause all kinds of weird performance issues with intake reversion near TDC.
It's a Formula 1 inspired race engine and it needs to be treated like one. Maintenance practices that folks use on lawn mower engines just don't cut it. :cool:
Setting the spring installed height is very important. If the installed height isn't correct you risk having too little seat and open pressure and won't be able to properly control the valve.
You can measure the installed height a number of different ways. One of the easiest ways to do it at home is to take a piece of .090 brazing rod or something similar and cut it to the exact installed height. The you can use it as a go/no go guage.
The Kibblewhite spring kits have a very good diagram showing where you to measure.
Most good performance shops will use a Rimac valve spring tester to verify each spring before assembling a cylinderhead. I've tested a LOT of valves springs and I've Kibblewhites to be very consistent and true to spec. You should have no problems just setting the installed height and assembling it.