Josh,
Mustangs Unlimited sells fenders, I'm not sure about the price though.
As for the Cobra spoiler, here's what needs to be done. The paint is sanded away from the currently drilled holes. Metal is spot welded to the under side of the hatch, and the sanded smooth on the top of the hatch. Then the hatch is primered and re-pained.
I just had this done on my Cobra when I installed my S-351 spoiler. It cost me around $400 to repaint the decklid, fill the holes, and drill new ones.
As for your rust, get some anti-rust protectant for now and spray it on.
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1994 Mustang Cobra
308ci, ported heads, Crane 2031 cam, Vortech S-trim 11#, FMS 1 5/8 headers, BBK Offroad H-pipe, 2-chamber flows, and several other goodies.
Rebel Racing. Home of Bay Area Mustangs