You do not need to cut the shock towers at all. I have a 1965 with a 351W that I installed in 1985, it all bolted in. The headers are nice, but stock manifolds will work. I am in the process of updating some with the Hedman Hedders and correct alternator and power steering brackets. You will need a higher capacity radiator for sure. The Mustang does not have a different crossmember from I6 to V8, the engine brackets bolt to the inner front frame rails, the tubular crossmember that runs under the engine is simply a brace from one side to the other, nothing bolts to it.
1965 Mustang 351W 4bl AT(Older brothers-I built it)
1965 Mustang 289 4bl AT(Mom's joy-I fix/upgrade it!)
1966 F100 428FE 4bl 4sp and 3sp MT