To answer your needle question it is 3 from the top or thick side. The more you raise the needle the richer it is.
Just my experience, I have Mark T's glasspacks and a K&N air filter without prefilter and I live at 6000ft. I talked to a rep at Factory Pro and was instructed to install 98s on the front two cylinders and 100s on the back four. He told me to set the needles at 2 on the back four and 3 on the front two. Of course the slows are 38s in this kit.
I found this setup to be MUCH TOO RICH! I was fouling plugs and blowing soot out the pipes. Even after setting the needles at the leanest setting and adjusting the pilot screws down to 1 turn out I was too rich by alot. I finally put the stock needles back in and currently run the pilots 1 1/2 turns out and it runs great

. Still a bit rich though and my gas mileage dropped from 36 to 30 mpg.
Ultimately, I think the Factory Pro needles are much too rich because of their profile. I like the 38 slow jets because of easier starting, no popping on decel, and more low end grunt, but you will suffer in gas mileage IMO.
So much for the reps at Factory Pro. I would look at anything they recommend with skepticism since they are in the business of selling aftermarket accessories.
To think that Honda got it wrong, and great strides can be made with simple modifications, is to deny the obvious.
The Honda Valkyrie is great Honda automotive engineering incorporated into motorcycles that will last and run longer than most every other motorcycle in the world, just like their automobiles. Who doubts that?
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