Disconnect and remove the battery. Remove the hood. Drain fluids (radiator, oil, and trans). Remove the radiator. That should keep you busy for a little while. Then, think about what else you need to remove to take the engine out. I made drawings as to how the wires were attatched to the starter relay and any thing else I thought might be hard to put back together later. Keep in mind that it will be months before you hook things back up to your Cobra.
FFR leaves the donor issues up to you...except the parts you need for the build...as they should.
As Doug said get started on the obvious stuff and parts you'll need, but I recommend also to start clearing away the clutter of what you don't need. Set up a Paypal account and start posting things for sale on corral.net/svtperformance.com/mustangforums.com/etc.....just do a google of forums to sell mustang parts. There's a whole underworld out there that wants what you've got.
Pull those seats..panels..console...etc....and tell people you got them for sale. Then snuggle up close with USPS,UPS,FedEx...not too close or your kids will come out wearing brown shorts or something. But the key is to start getting rid of those donor parts and making some money for you to sink back into the build.
FWIW don't underestimate the shipping costs and make sure the buyer pays it.
I'd usually sell stuff about 40% off what a new part costs from http://www.parts.com/partlocator/index
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