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