Some cranks just cant be trued up perfectly.
If the crank pin bore centers are not exactly the same offset from the center line of the crank then you'll spend all day knocking it back and forth.
If you're left with any runout, make sure that it's inline with the crank center and the pin bore, and on opposite sides of the crank. That's about it.....put the kettle on.
Here's a quick rundown for a single cylinder crank:
If the runout is on the same side of the crank then the crank's either spread or pinched, so you need to spread or squeeze it. Always do the spreading or squeezing as far away from the crank pin as you can.
If the runout is at opposite sides of the crank at around 90 degrees to the center line of the crank and center of pin bore then it's twisted, and needs a wallop on the low side.
It sounds easy, but gets more frustrating as you get it closer to true.
An NSR crank is not much different as long as the center wheels are indexed accurately in the first place. But it does take longer. You can get them within Honda spec pretty quickly, but getting them on the money is a different story. But it's worth it as the engine makes more power after peak, revs harder and the crank lasts longer. Why wouldn't you do it?