I know the GT40P heads require a special header, MAC makes a set along with some other brands. For mine I also had to use 90* boots on the plug wires for them to clear, other than that no problems. My car is a 68 so I don't know about any clearance issues on a 65.
Like he said...special headers, or hipo cast mainifolds along with 90* boots.
I did end up drilling the heads to match the steam holes in the block though, made a big difference in keeping the car from heating up in traffic. Prior to that, it would creep up at every stop in 115* heat (muggy South Carolina weather). After drilling out the holes above the cylinders, stayed cool quite well, at least til lately, but the radiator needs replaced now, crudded up pretty good.