Some of the things that you'll need:
Your shock towers have braces that go to the firewall. They will not fit around the 5.0 HO airbox. You will have to get a purpose-built brace, or replace the fuel injection with a throttle body or carburetor style intake to resolve that.
Your oil pan and pickup will have to be changed to the earlier front-sump version so it clears your crossmember. Dipstick will have to be installed in the front timing cover and run up through the alternator bracket. The side hole for your dipstick will need to be plugged.
Your rear end (7.25 inch probably) will not do well behind a V8, especially one with as much torque as a 5.0 HO. The 4-lug hats on your car should probably also go away in favor of 5-lug, to handle the additional stresses and loads. Your donor car rear axle will be an 8.8 most likely, and will not be the right width, nor have the proper spring perches or mounting points for your car. There's a lot involved in swapping in an 8.8 to an early Mustang, and would take up too much room to describe here. If you somehow have an 8" or 9" rear end, you'll be fine.
Your front springs are soft, and may not provide enough lift to keep your nose where you want it, during spirited driving with the heavier V8. However, they do provide a very smooth ride, and some V8 drivers actually use the old I6 springs. Your call. The swaybar up front should definitely be upgraded to a 1" unit, to prevent body roll during cornering, and I would strongly recommend the Shelby drop - although these two upgrades apply to any vintage 'Stang.
If you choose to keep the flop-hat EFI setup, I recommend that you actually put the air intake on the driver's side (reversed from normal) because that will allow you to use your existing throttle linkage to actuate the throttle plates, instead of a cable-pull setup. You also have the added advantage of being able to run the mass air and air filter up to the front where there is no battery to interfere. Setting things up this way will mean a bit more work with a stock EFI harness, but it is in many ways a much better setup. The factory Ford EFI setup is excellent for street-driven cars.
Whether you are using a C4 transmission, or a manual, you need to make sure that your flywheel or flexplate has a 50 oz imbalance, and the correct number of teeth. The balance is dictated by the engine, the tooth count by the transmission. All smallblock '67s used 157 tooth, as far as I know. Your I6 transmission may be different. If you are keeping the transmission from your donor car, then you will need to deal with a transmission support, and you may have to have your driveshaft cut down and rebalanced, or buy a new one of the appropriate length.
Ford's AOD transmissions will require a TV cable setup in order to work. It will burn up without the TV cable being properly calibrated and set up. The 4R70W is in every way a superior transmission, but also requires an electronic controller to set up. Both of these transmissions work quite readily with the existing automatic shifter, and should be low-fuss to set up.
The shorty headers that came on 89-93 Mustangs may have fitment issues, especially on the driver's side, and with power steering. Factory '67 cast iron logs fit great, but not so good performance wise. The 289 Hi-Po manifolds aren't too bad. Tri-Y headers fit easily, and offer excellent performance as well. Scott Drake makes some stainless steel headers that might be a good choice for you. Once you've selected the headers, you'll need to have exhaust fitted. 2 1/4" exhaust is probably going to be your best choice for a 5.0, even with mild mods. Make sure that you include an H or X pipe in your exhaust, to help equalize pulses between the cylinder banks; it should help with economy, power, and even make the car sound better.
Up front, you will need to decide what to do about your accessories. I recommend that you keep the 5.0 equipment and reverse-rotation serpentine belt, as you can run a better alternator without belt slippage. You will also be able to do away with your original voltage regulator, because modern alternators are internally regulated. The fan and its distance from the radiator are critical, and the big plastic fans that came with 5.0 HOs don't work well. You can purchase aftermarket reverse-rotation fans that will probably bolt right up to the 5.0's fan clutch, and look much more like a stock '67 piece, as well as fit the radiator shroud.
You will need a V8 type radiator with the inlet on the upper passenger side, and lower driver's side outlet, to match the water pump of your engine. If you have an automatic, make sure your radiator has fittings for the coolant lines for your transmission.
I'm not sure the I6 Mustangs in '67 came with a dual master cylinder setup. If yours is a single-bowl, you would probably do well to upgrade to dual, in the name of safety. Your front brakes and spindles should also be upgraded to discs, for the same reason. There are many many choices here, but if you're interested in keeping stock style wheels, SSB has some very nice kits with Kelsey-Hayes style four-piston discs that will work fine to stop your car, and allow you to keep 14 or 15" rims.
There are many more little things I'm sure I'm forgetting, but those are all the big ones I can remember! Hope it helps.
