My GT40 was an OEM Cobra. IIRC to do the swap you do have to use the 1" spacer and you will have clearance issues with the stock tower brace if you have one. And you should probably be running a setup that puts the air intake in the fender anyway, otherwise its just sucking in hot air from the engine compartment.
2000 Mustang GT Steeda #0048 34k miles. 99 Cobra 4V swapped, FTBR IRS swapped, exhaust, tuned by James Gordon.
Just because I give you advice, doesn't mean I know more than you. Its just means I've done more stupid ****.