Ugg one more year older and you wouldn't have this problem. This is common problem as 351 is very tight for a 64-66. I would never cut on the shock towers unless you bring the stability back in through welding. Both Hooker and Hedman make headers for this specific swap, I think that will be you best bet, though not cheep.
-by the way I have a 58 ford f100 with a 289
-by the way I have a 58 ford f100 with a 289