I think it starts with deciding on new long tube headers or staying stock there and I don't know any shorty header options for the 4.6.
My all Magnaflow setup is pretty good in it's final configuration for my 5.0. Two rear mufflers, DI/DO resonator, and high flow cats if you want it to smell better.
I'm not sure what to suggest if you have to pass inspections.
1992 Tbird LX 5.0, 3.73 gears, 1995 Cobra intake, deleted air silencer, 2.5" mandrel bent dual exhaust, SCP shorty headers. Updated four-hole fuel injectors. SK shift kit in AOD. Vogtland 0.9" springs, Tokico and Bilstein shocks.