Might want to think about a set of Denso spark plugs if you don't have them already from when they installed the SC. They should help prevent any high rpm spark blowout under boost and prevent a misfire. A single blade TB maybe would be a fun swap. Or an aftermarket shifter or X-pipe. Other then that....? umm, maybe change your oil or something 
BTW, what shop up your system? and did they also tune it?
I would love to check out your car, so if you are ever going to be hanging out in town, shoot me an email at jackthemacksnip.net.
BTW - for other's reading this, if I remember correctly he has a '99 or '01 Cobra with an aftercooled Vortech setup. AM I right Rice Hunter?
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'97 T-bird LX 4.6L 2V, auto
SVO heads/intake, Vortech T-trim, front mounted intercooler, blower cams, Cobra crank, Manley H-beam rods, JE pistons, Aeromotive fuel system w/ 42# injectors, and much more
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