eh. I favor the long tube headers more myself. I don't know that the short tube ones give you any sort of scavenging effect. But, that's all debatable since header design is such a "black magic" kind of art.
It is going to flow a lot better than the stock one, thats for sure. Don't know that you'll notice a whole lot of difference between the greddy one and the one you have now. Might make for a touch better low end torque, but I wouldn't expect any high rpm gains.
You're on the right track with the flex pipe.
I have also seen where people have cut the flange in between each runner to give it some flex relief. And also reinforce the welds, especially the collector since that is the key area to crack.
The general masses are split between the greddy and the hotshot headers. Some really like the greddy one, and others say the hot shot is better and made more power.

I'm thinking I would more than likely keep the little section of down pipe you would need at 2 inches. I think. Maybe 2.25. too much larger and you run the risk of letting the exhaust gases slow down. That downpipe is supposed to go where the stock cat is located. If you have a cat, that would be the best place to step up to the larger exhaust pipe.
I don't know how I feel about a 3 inch exhaust. I personally would not go that big for a NA build. Maybe for a turbo built. Depending on the size of the turbo. 2.5 might be too restricting for the turbo to spool up nicely if it is a decent size. But even for your supercharger, I don't know that I would go 3 inch. Just feels like overkill to me. For me, if you're using an off the shelf header, then I wouldn't go over 2.5 since all of the off the shelf headers I've seen have collectors either 2 or 2.5 inches. If you are going to go the custom header route, then I would say it depends on what the ideal runner diameter is. Crunch the numbers, get the ideal diameter of the runners, and the collector and base the rest of your exhaust on that.
Too big of an exhaust allows the gases to slow down more, which can actually create more resistance than a pipe that is a little bit too small.