Don't know why the link doesn't work for you, it works fine for me, the text goes straight to Downloads. There are quite a few threads on tuning VM carburetors on the site, and a quick search should give you plenty of information. Here's another source, the 26 page Yamaha 650 Society carburetor manual. It's as complete as I knew how to make it. It's the property of the 650 Society and the price is $17. To order a copy, send a PM to desmoman900; he's the director of the group.
Understand this: there is no standard recipe that's going to be right for every motor. You need to give the motor what it's asking for, all anybody can give you at a distance is a baseline to work from. You need to look at more than pilot and main jets. If you have the generic Q-2 needle jets in your carbs, replace them with either P-5 or P-6 needle jets. Most of us have the best luck with 6F9 needles. The pilots and mains that you have are a good starting place.
Best of luck to you.