if you are going to do a custom exhaust why not buy longtubes, then do custom dual or whatever it is that you had in mind?
The answer to your question is yes! a tuner cat turn off your rear O2s and that will keep the CEL off! Most tuners charge $250 and up to do that
On your Gen 4 5.3, a set of longtubes ( $350+ ) with a 3" single system or 2.5" dual system with a full tune will really wake that motor up? and it will sound better. It would sound awesome with DOD Delete kit and a cam... Just throwing that out there
Yea I've got EFILive on it now with the DOD deleted so maybe I can sweet talk them into deleting the cats. Ha. And what brand of headers do you guys recommend?
Id go stainless if you can afford it, but it depends on your climate! I am running the pacesetter longtubes and I have not had a single issue with them! I live in central texas and we "typically" don't have a lot of rain, so I have never worried about them rusting through! I have had them about 6 years now and they still look great ( other then where I have smacked them on speed bumps from being lowered, but that is my fault, not theirs ). I have the corresponding Y pipe and it fits nice too.
So did you do an actual DOD/AFM Delete, where you pull the heads and replace the lifters and all that jazz? If that is the case then a simple cam kit would be a pretty easy job.
HP Tuners is the popular software used for Gen 3/4! I have never messed with EFI Live but I know guys use it and I am sure what you are wanting can be done with that software