i was faced with that very decision a few years ago. i had a 351w block with plans to build it for my 66 mustang, and put a 289 in my 64 falcon. in the end i decided to keep the falcon a six cylinder car, so i had two V8s for the mustang. i chose the 289, it is lighter, a bit more compact, and can make good power with decent heads and cam, plus it out revs the 351w due to its lighter rotating components, and less friction.
the 351w will fit the 65-66 engine bay with headers, but you do need swap headers, and they cost money compared to the headers for a 289. and with the good aftermarket heads available today, i wouldnt use the cleveland heads to make a clevor engine, they just arent needed these days. if you want to use them on something, put them on the 351w, and build that engine for something like a torino or 66 or later fairlane. or have some real fun and build it for a 66 or later falcon two door sedan. these cars have the room for a 35w/c clevor engine. at the same time stroke the 351w out to 393ci, use the stock 351w rods and stock 302 pistons for a budget 393 build. keep the horsepower at a reasonable level, about 450hp, and have a motor that will live a long happy fun life.