I don't diasgree with you guys, you just have to try it out till you get the jetting right. There are so many factors that has to be taken into consideration in addition to the air filtering and exhaust, like altitude and air humidity, so there is no way to tell what size will work best before you can test ride the actual bike.
You just have to have in mind that the 650 carbs was originally jetted very lean from the factory. With the stock jetting they had a slight stumble in the 5000 rpm area, and if you snapped the trottle wide open, there was a flat spot. This is mentioned in several test reports from the periode. And the recommened cure for this problem, at least in England, was to go up on the main jets from 90 to 98, with the stock exhaust and air filter. Then add pod filters and a 4-1 exhaust, and it is impossible to tell in advance what main jet size that will work best. But by putting on pod filters you can also face other problems, like a leaned out mid range and idle mixture. And if you have the CV carbs, they don't always work to well with pod filters at all.