The best place to start with a Mark is with either a chip or a j-mod to firm up the shifts. The chip will also give you better timing to pick up a few ponies. Also add a tranny cooler to prolong its life.
Then I would go to the IRS and drop in either a 3:73 or 4:10 pumpkin with "posi". Dual Exhaust from the cats back. Minimum 2.25". 2.5" if you plan on a power adder.
Then power adders. Either a nice 125 shot or a Vortech will work. I haven't seen huge gains in the cam, intake side of things. Sure, you can pick up some hp with an intake swap, but I would save the coinage and just stuff an extra lb of boost thru it to make up the difference.
And yes, '96-'98 Cobra is the best way to describe the motor, etc. in the pursuit of parts.