Blindsight,
As I remember, you had a stuck #2 on a CB500 or CB550. As long as you have it apart, I highly recommend replacing your valve guide seals and lapping the valves. It really does make a difference for power, smooth idling, even power band, possibly blowby past the valve guide seals, and a minor impact on oil consumption. These engines are pretty robust, and will run even if they are in a bad state of repair, but the more you prepare your engine now, the happier you will be down the road. It REALLY makes a difference to do it right from the start... trust me.
Regarding your cylinder head, pull the valves, pull the valve guide seals, lap the valves, replace the seals, and reinstall the valves. You will need a valve spring compressor (I recommend this one:
http://www.amazon.com/Tusk-Valve-Spring-Compressor/dp/B0039L9GAC/ref=sr_1_11?ie=UTF8&qid=1296611378&sr=8-11), valve lapping compound, and a suction cup tool to grip the valve.
If you do not replace the valve guide seals, then you risk a lot of blowby going between the valve and valve guide and pressurizing your engine. The greater crankcase pressure won't really do much to the operation of the engine, but you will see greater smoke coming from the positive crankcase vent hose, which is pretty stinky and will make your pants smell. Your engine oil life will decrease too.
If you do not lap your valves to get a good seal on your intake valves, then you will lose some power (could be substantial), blow the charge back through your intake system (which will screw up idling, smoothness throughout the rpm range, and make the engine run pretty roughly no matter what you do).
If you do not lap your valves to get a good seal on your exhaust valves, then you will lose some power (could be substantial), and you will notice some rough idling.
This all adds up to a smooth running engine that doesn't die when you roll of the throttle, is easier to modulate power (especially nice when you are in traffic), and also an engine will not leave you smelling like poorly combusted 87 octane and eau de 10w-40.
Your engine will run if you don't do these things, but I can almost guarantee that you will be happier with your bike if you do.
Also, make sure you use a good sealant when you apply those rubber pucks on the cylinder head. Don't use RTV. Three-Bond works well.
Camelman