As far as computer problems goes, You will only throw o2 sensor codes.
If you are removing all the cats I would recommend replacing them with High flow cats, or replacing the muffler with a better one. Because with the way the ford heads were designed, They need back pressure, and if they don't have the back pressure that they need, you will eventually get head knock. Which isn't fun. I've been through it myself on my 98 4.6l. In all honestly, these engines run better with the cats still on them. If anything at all, I'd just gut the cats.
Right now I'm running high flow cats by flowmaster, 2.5" pipe into a single in, dual out super 44 muffler from Flowmaster. I don't have any piping coming out of the muffler it self, and it sounds pretty good.