Thanks for the responses, guys. This motor is going into a 63 Galaxie boxtop survivor that his 77k original miles and is in fantastic original condition, so that's the reason for not wanting to cut or reshape the inner fender wells.
While the car's purpose is 95% cruising, I don't really want to give up that much HP on the top end with shorties. It's going to be hard enough as it is to get traction down low so increasing the low to mid range torque with the smaller primaries isn't super critical. Chilly is right about the cost of the build, so losing some of that power I'm paying to make would be a shame.
If anyone here is running longtubes in a 63/64 Galaxie, I would love to hear what you're running and if you had any fitment issues. In the end, if a compromise needs to be made, it's likely going to be in the form of a low hanging collector that otherwise fits well...just don't know yet what header fits that bill.