A couple of thoughts on the engine cover/engine interference:
Usually it is the hinges on the engine cover hitting the fan shroud. If THAT is what's happening, flip them side-to-side to push the arm out farther to the sides and they'll probably fit.
If it's the underside of the fiberglass cover then, Yes, you can notch the bed pan to fit.
But another thing to consider is going to the newer, better-cooling 1971 and later engine fan shroud. It is flattened on the top so it doesn't stick up quite as much so it won't hit. It also has a bump out on the back to accept the larger, later oil cooling tower. You should also get the slightly larger fan to go with it.
Bugcity.com usually has good used ones plus the fan and tower.