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.
We don't even have a real long tube option. There are the super rare and uber exotic rebuilt Mac Long Tubes from Guitar Maestro, where you have to modify them to clear the steering shaft. Shorties have demonstrated no measurable gain on the MN-12 platform, and the Kooks are $800, and are actually "mid length". I'll be saving up for some of them while I'm working on a new motor.
97 Thunderbird LX (The GT Bird)
2003 Explorer WAP block with Modular Head Shop "street ported" heads and Stage 2 PI NA cams, 75mm Accufab throttle body, C&L upper intake plenum, Kooks 1.75" primary/3" collector headers, 2.5" full exhaust with mid mount Magnaflow dual in/out muffler, 24lb/hr injectors, 80mm MAF, Tuning from Don @ www.lasotaracing.com
, CAI that feeds from fenderwell. Jmod, 3.73:1 TL in Mark VIII carrier, Mark VIII aluminum LCAs, 93 Mark VIII driveshaft, PBR brakes (soon to be Cobras), 18x9 wheels with 35mm offset, 255/40/ZR18 Tires, Front and Rear strut/shock bracing, GR-2 shocks, Eibach 1.5" springs, 1989 SC front and rear sway bars.