Joe,
My system is setup similar to yours in that it connects to the original cat flanges. I've got the Kook's headers on order and have the cats already. The same shop that did my custom cat-back setup will be welding up the flanges and O2 sensor bungs to the cats. Since we both have OEM flange positioning, I could possibly get a second set of cats put together for you when I get mine done. That way you would be able to just bolt in your system.

I believe can answer some of your questions however. 1) I personally think your low end torque will be better with the 2.25" system and top end hp will barely be affected. 2) I don't think they are flanged the same based on pics I've seen, but my comments above may help with this concern. 3) Yes, they are coming out with stainless now, and all future production will be stainless. That is what I ordered and I think it's a great idea. They're a little more expensive but I think they're worth it. They'll last forever. 4) No longer a choice.

Thanks for the hanger tip when I put my system together. They're much better than the '03 hangers.