the stocker will flow enough CFM for around 500HP and will more than keep up with a chipped 6.0 it is when you get sticks and a bigger turbo you have to change.
i would have to say the mods are mainly based on what YOU want out of the truck...I dont want to buy a 40k truck every 5-10 years so i opted for the oil bypass and coolant filter system...both very important also will be adding a fuel cross over line soon.
I believe i have seen Biller alum caps for both the upper and lower filter canister in a set for like 80-90 bucks...they are pricey...amsoil sells them and you can get them directly from racor's web site as they are the ones who make the filter assy...try to stay away from cheap no namers...
when i did mine i did not really notice a increase in MPG it is mainly for Sound and Lower EGT's But on a SRW truck i like Singe on a DRW i like Duals with 6" tips.