Man, what a nightmare. I have absolutely no idea how anyone was able to do this by themselves, but I commend you. I had a car buddy helping me and it was still a mess. Long story short, we did everything by the book and my driver header is on without two of the bolts because they didn't fit because of the design. We managed to get 5/6 of the passenger header bolts on, but since the BBKs aren't threaded where they connect to the cats, the bolts didn't line up once we FINALLY managed to get the cats to meet the header.
So, my car has an exhaust leak that sounds like a dragster, it's just one cylinder I think, maybe two. My passenger side cats are being held on by one makeshift smaller bolt with washers on both ends, since the BBK holes wouldn't line up and we had no other options at the time.
I used tips and guides from other people, including dousing EVERY bolt with PB blaster and letting it sit, removing battery and tray. We did it with only one ratchet extension, so that's definitely partly our fault but did everything else people recommended. I'm going to need to either find very short bolts with the same threading to fill the missing holes on the headers, or just take this to a shop to have them clean up the mess.