Shaving the head will gain you more compression. Shaving the head also straightens the head if it's been overheated and has warped. If you're already bumping up the compression with pistons AND shaving the head, you may end up with too much compression and be forced to run high octane fuel. Has a machine shop checked the block & head to make sure they are straight? Make sure you're starting with good parts before you put it all together. What are the stock compression numbers compared to the high compression piston numbers?
Decking the block refers to machining the engine block so the piston height is maximized at TDC.
You could port match the intake & exhaust on the head with a die grinder. Take your intake & exhaust gaskets, place them on the head (after lining up the bolt holes), mark out the material you can see on the inside of the gasket and then remove the material up to the gasket. After that, try blend in the intake & exhaust ports further into the head for the best flow. The smoother, the better. Obviously you will want to disassemble the head totally and clean it up very, VERY good to remove any small pieces of material. May be best to have a machine shop clean it up after you've done some work to the head.
A 3 angle valve job is a good thing too, pretty common when you have machine work done.
I have no idea how well a Samurai head flows, but I would imagine there could be some small gains. Most of the difference may be at higher RPM's though, since you'd be opening up the ports and reducing velocity at low RPM's.