The heads/intake is an absolute must for staying NA. You can get the FRPP aftermarket heads and intake or you could also get the heads and intake from a 99/00 4.6 SOHC, those will work as well. Get the heads ported and polished would be even better (99/00). Of course the no silencer/K&N combo, underdrive pullies, the stock MAF on the 4.6 SOHC is 80mm but has the little post in the center acting as a bit of an air restriction so you could get an aftermarket one without the post, aftermarket TB only after you get a different intake (stock intake is too restrictive), ram air is an option (I route mine from the passenger side fog lamp location cause I don't have fog lamps), WEIGHT REDUCTION- these SN95s are heavy!, exhaust:headers, H- or X-pipe, catback if you like (like was mentioned earlier those six cats are VERY restrictive), gears: I've heard 4.10s recommended for the automatic/3.73s for the 5-speed daily drivers (gas mileage the factor) and a steeper gear for the drag racer 4.30s auto/4.10s 5-speed this is cause the 4.6's power band is higher in the revs than the 5.0 and the car/engine weighs more than the 5.0 so it takes a steeper gear to get the car around and to get into the power band. I can't think of anything else right now. Hope this stuff helps.
Good luck. These 4.6s are a bit more expensive to play with but still fun all the same. Have fun!!
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1996 Mustang GTS: 5-speed, K&N, removed air silencer, 3.73s, turndowns after stock H-pipe (no mufflers)