I have a 1995 cobra. I'd start off with under drive pullies, cold air intake, DIFFERENT GEAR'S, Headers, I was told they come with forged internals from ford. If you you stroke the motor I'd get different head's instead of the "gt-40's " iron heads that come stock. The "gt-40" upper intake, lower from ford wont handle 500+. Trick flow has a nice kit along with edelbrock. Some people dont like long tube headers because it's a pain in the ass to install. But in your case the motor is out so it will be easy to do. But with any header I'd pick a ceramic coated kind " better for heat control" If you go 500+ horse I dont think the t-5
tranny will handle the power, along with the clutch. With a 347, and a super charger you should be around 500+