A higher lever of a practical, smooth power is what will give you a 450 4t killer. Unless you're a duner or race HC.
Make it all top end, and you will get nowhere fast. I'm not setting out to denigrate your riding ability, but even the best riders in the world would get nowhere with just a top end oriented 500. If you can go genuinely fast , for any length of time, on a bike such as you propose, get thee to a factory team, now.
Mikunis are difficult things to deal with. You'd be much better off with a 41.7mm Keihin.
It's not hard to get a lot more power than a 450 4t with a 500cc 2t, smoothing out the power delivery is what will get you places.
How old is the barrel? - I'm fairly sure the 86 and onwards water-coolers had the diaphragm PV. Perhaps you've an AC barrel conversion - I don't think I ever saw a factory PV'd AC barrel.
What made the 490s/500s so good was their usability. Not that they had the most power - Honda spent quite a few years making the CR500 more ridable.