Okay so I picked up a range of main jets and a new 55 pilot in I end up needing it. My stock pilot, 52.5, had no side holes and a very very tiny hole. The new pilot however has a hole three times the sizes and eight side holes drilled into it in vertical pairs. I mulled it over with my bike guy and he swears up and down that it's the next stage up. Being that my family has been working with him for 25+ years on bikes I'll have to believe him but is the upgraded pilot jet really that much more open than the stock jet for a 99 bs40 carb?

Go with your bike guy's knowledge/suggestion.

I swapped mine about a week ago and this is what they looked like...(I boogered up the stock jet's head by trying to turn it the wrong way  )

I picked mine up from a local bike shop that dealt with mostly import bikes. If you find one just ask them and say you have a mikuni bs40 that you want a new pilot for. Shouldn't be more than two or three bucks each. When you step up on a jet size some will have bleed holes as was told by my mechanic. I'm running the 152.5 and #55 jets now with grand results

The 55 that I have has bleed holes in it. If you look at the pic that EJID posted you can see them.