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Take a look over at the 4.6 forum @ FFCobra, you will be able to pick up a lot of insight from the 4.6 builders.
http://www.ffcobra.com/cgi-bin/ultim...=0;DaysPrune=0
Using a complete donor car will be the easiest/least expensive route. One the greaest challenges will be dealing with Ford's PATS system but that has been taken care of! 
Good Luck!
Pat
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Proud owner of FFR1004630RD '01 Explorer 302, FRPP B-Cam, Holley S/A 670, HD T-5, Wilwood pedals, 3 link, Koni shocks, 17" Bullett wheels, Baer brakes, Classic gauges, I-Squared wiring, Jaguar Racing Green w/Sliver Stripes
Tagged and road ready in NYSas of 6-5-09 Life is GREAT!
My build log http://www.clubcobra.com/forums/cobra-build-logs/80663-my-cobra-build.html
If you live "Upstate" near Albany, NY send me a PM. Our Cobra gang is growing and looking for new members!
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