Congratulations on finding a nice looking fastback. In my humble opinion the '65 - '66 2+2 Mustang is one of the best looking cars ever built, then again, I'm a little bias.
Tell us what your ultimate plan is for the car. Obviously, you're not building a concourse restoration, because you're already considering changing the interior. Are you building it for a daily driver, weekend warrier, show car? Do you have any interest in drag racing, auto cross, or road racing open track events? Also, if you start a new topic for each specific item of your restoration, you're likely to get more responses with specific answers.
First off, if your going to restore/replace the interior take good notes as you disassemble. Write down the sequence of events as you take everything apart and bag all of your screws and small hardware in ziplock bags clearly labeled. Have your final game plan in place and plan for your final product.
Next I would go through your wiring and clean up anything that any of the previous owners may have hacked up. Then pull your new wiring for any future electronics. I would consider installing an auxiliary circuit block, like a Painless 7 circuit fuse block -
http://store.summitracing.com/partdetail.asp?autofilter=1&part=PRF-70207&N=400012+115&autoview=sku Try to think what electronics you might be adding: Stereo (1 constant hot, 1 ignition hot circuit), Alarm (1 constant hot), Stereo Amp (1 constant hot, 1 ignition hot), Power Windows (1 ignition hot), Power Locks (1 constant hot).
Next, when the interior is completely out, get some good sound deading insulation for the floors and above the headliner.
For your carpet, you can order any color and type of carpet you want from Auto Custom Carpets -
http://www.accmats.com/ - They custom made me a plush cut pile carpet, heated molded for my car and it only cost $10.00 more then buying the stock heathered loop from one of the venders. Also, forget the stock and reproduction door sill plates, they are way to flimsy. Scott Drake finally came out with a Stainless Steel door sill plate that is much thicker and more durable -
http://www.mustangdepot.com/OnLineCatalog/Interior/door_sill_plates.htm
Take the old stock seats out (and store them) and get some new style seats. They will be much safer and more comfortable. Start a new thread, just on seats, and you will get a ton of good ideas. I sprung for some new Corbeau CR1's in black leather -
http://www.corbeau.com/products/cr1/cr1.shtml
For your stereo, I say go ahead and cut the dash and install a good quality head unit. I've got the top of the line, over priced, Custom Auto Sound Kenwood Cassett Player, CD changer ready, receiver - and it is a total piece of Sh_t. I do have some nice Infinity Kappa 6X9 speakers mounted in the rear lift up panel.
And some componet speakers up front. I installed the woofers in the kick panels and the tweeters in the hole left by removal of the window crank (when I added power windows).
Power windows are a great mod to do.
I installed the window switches in the console.
Sorry, I got a little carried away. Also, I removed my back seat and made an amp rack and tool box holder. I've got pictures of the process if your interested.
Good luck and welcome to an addictive hobby that will suck your bank account dry,
Tim