One way to make a clean dimple, if you've got the room to swing a heavy hammer.... take a piece of thick wall tubing that is big enough to fit over the steering shaft, cut a piece a inch or so long, then split it length-wise making 1/2 of a sleeve....lean motor over away from shaft with big lever, slide cut tube halfsleeve over shaft then let motor and header come back tight to the tube halfsleeve and shaft and hold it pinched in place. Smack the opposite side of the shaft with the heavy hammer and this will leave a small curved dimple in the tube. Remove the sleeve. That 1/16" dimple should be all you'll ever need unless the motor mounts are shot.
By chance are you still using rubber motor mounts, and not polyurethane??
Heating and prying is likely to leave an ugly nasty looking clearance point, especially if they are coated. Done with something to make a smooth dimple like I suggest, if possible, will leave even coated headers intact, especially if you pad the sleeve with a layer of electrical tape.