You will need a new k member, and stand along fuel system to say the least. Will probably need a tranny as well. it's been covered on here several times and I had a friend that did it. Long story short, for the money, time and effort, he wished he would have stayed with a 4.6. That would be my...
Another thought, I notice on a lot of Mustangs that the accelerator pedal is close to the transmission tunnel and, over time, a hole can wear in the carpet and insulation letting more heat into the area.
K member, computer, engine, trans, trans k member, drive shaft, entire hyrdroboost system, wiring harness from firewall forward, probably the dash harness, instrument cluster, computer, exhaust, off the top of my head.
Drop base on the air filter. 1 1/2-2 inch filter element, GT hood and clearance it under the hood scoop. Hopefully you can still get enough air into the carb. You can play with the height on the filter element.