Personally I would not deal with the hassle of putting a late model engine into a classic car. Plus the modulars are massive and the 66 couldnt really fit anything that big in its engine bay though im not 100% positive if the 4.6 would or wouldnt fit. I remember reading an issue of Mustangs Monthly where some actor had a 66 or 67 with a late model motor in it. You might want to look for that it might have some info in it about how to go about doing it.
__________________ Black 2006 GT T-2 Torsen Diff, 3.73 gears, FRPP 90MM CAI, SCT X-Cal 3 tuner/ Speed Inc. dyno tune, FRPP catbacks, Steeda Triaxe w/ Hurst stick and T handle, SVT strut mounts, FRPP strut brace, Steeda UDP, JBA long tube headers, JBA O/R H-pipe, CHE LCAs, CHE anti-squat brackets, Steeda adj. UCA, FRPP blue valve covers
304 rwph, 322 rwtq
1968 Convertible PROJECT candy apple red 289 2V (swapped to edelbrock 600 cfm performer and performer intake manifold with a mild cam) | 
4.6l sohc swap into 66 mustang 
