Are you using an aveo clutch or a 2.0 clutch?
Why not just drill out that 3rd CAT hole, then the rest of the exhaust should fit without issue.
Keeping A/C? Pictures and a write up with a list of everything needed to do the swap would be awesome. If you wouldn't mind, I would love to put the writeup on my website under the tech articles at www.uniquemotorsports.com. The site has been up since 1999 or so and probably will not be going anywhere anytime soon.