You have a computer controlled engine, so there's not a lot of "extra" vacuum lines like the non computer models. You should have the thermostatic air cleaner, the air pump, hvac, PCV, EGR, canister purge, and a heat riser (EFE) valve. Really, all of them need to stay, the only two that wouldn't affect emissions directly would be the EFE and ThermAC, but then you'd have lousy cold running.
Replacing the old lines is a good idea, I think you will notice a better running engine without all the vac leaks. And at the same time you can make things neater.