FWIW - I just did something similar this past Wednesday to my 2003 n/a Baja. While I did install an ebay/Borla header, I kept (replaced) the 1st cat with a new stock unit, eliminated the 2nd and 3rd cat, along with the stock resonator. I replaced the stock muffler with a Magnaflow (part 14830), and used 2.25" piping from the cat back. While the sound is incredibly deep, growly, and just beastly, it is also ridiculously LOUD
. The droning inside the car is deafening, even at slow speeds. I am going to call the shop back on Monday and ask what the largest resonator (glasspack) I can add back in!
I did not notice any performance gains or losses with the reduced back pressure, and the car seems to run fine. I thought I may get a CEL from the increased flow through the cat, but nothing so far...