351W in an early pony body

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first the fit is rather tight, but quite doable. i recommend swapping to 66 mustang mounts as they set the engine a bit higher in the engine compartment making header clearance better. use a good set of shorty swap headers as they will fit better than long tube headers, and you wont notice the performance difference. use a performer rpm intake with an edelbrock carb and a drop over base air cleaner for hood clearance. again it will be a bit tight but this combination clears the hood. if you have any qualms about ubsing the rpm intake, then use the regular performer intake as it is even lower. when you swap to a 5spd, i highly recommend that you also swap to a cable or hydraulic clutch system, as the stock linkage tends to bind. consider installing an electric fan to replace the stock one as you can gain some clearance between the engine and radiator. use a good 3 or 4 core radiator, i prefer copper/brass rads but if you want an aluminum one make sure you get one with at least 16 fins per inch, and two rows of 1" or 1.25" tubes.
 
Couple of things,

1) the 289 and the 351w are the same length, so there shouldn't be a fan clearance problem.

2) just for ease of future under the hood work, I would consider shaving the inside of the shock towers to add a little width. they are pretty generous with spring clearance, so you should be able to gain atleast an inch on each side. I have even considered swapping to a coil over arangement to add even more room. Again this is not required, but it would make your car alot easier to work on in the future. Just a thought.