Yep, motor,
tranny, rearend for sure. I'd swap to a 5-spd (the auto's are weak). The rearend will swap although you'll have to swap your Mustang axles into the TC rear and buy offset caliper brackets to run the rear discs. TC's don't have a 3g alt, although it'll work. Front brakes - yes but you'll need the TC spindles (they fit), the sway bar will bolt on but it's too wide. Go to the junkyard and get a 5.0 bar, fits perfectly.
Radiator and fans may work but you'd have to do a lot of fabrication. There are better combos out there. TC bucket seats will fit as will the restrictive air cleaner assembly. I see you're in California. You'll need it too pass smog. Also the EGR solenoid valve will be required. The VAM connector along with at least 6" of wire to splice into your existing wiring harness. That's about it off the top of my head. Sell the rest of the parts on NATO or Ebay and make some $$$!
Almost forgot! You'll need the LA3 computer also.