Start with the proper float height. Verify that with and actual check of fuel level with a clear tube held against the carb.
After that, I have heard conflicting reports on the order to tune, but my (semi-)logical mind says to do the idle circuit first. Why? Not too many people are able to start a bike and immediately go to wide-open throttle to check the main jets. Somewhere, you are going to have to use partial throttle to get down your driveway to the street, then get to your testing area. Unless, of course, you have the luxury of doing your jetting checks at a drag strip or a dyno room.
Your pilot jets don't really care what the main or needle jets are. They are the smallest, most-restrictive jets. Yes, they happen to get their fuel through the main jets, but you could remove the mains without affecting pilot operation. The needle jet also draws fuel through the main jet. However, it is much smaller than the main jet, so it also doesn't care what the main jet is, or even if it's there.
<My> preference is to tune from the bottom up. Set the fuel height. Get it to idle. Get your low-throttle and mid-range operating properly so you get get to your main jet testing area. Then get your mains dialed in.
My opinion. Could be wrong. You are getting your money's worth.
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