There are a few options you could explore. When that happened to me I replaced the factory cat with a Magnaflow 2-1 piece (P/N 94007 I believe), welded to the factory mid-pipe and connected to the pre-cats with flexible tubing. I don't entirely recommend this approach as the pre-cat pipes aren't entirely circular making a seal quite difficult. Also the flex tubing isn't very robust and I had to replace it once or twice a year.
It may be possible to use some repair flanges, like these:
If there is enough sound metal remaining these could be welded on in place of the original flanges.
The most expensive but probably best/longest lasting solution would be to have an exhaust shop build up a replacement. They could add a resonator in while they're at it if you were so inclined. This is the path I went in the end to resolve the problem for good.