An EZ Out set might already engage the set screw without drilling. Try that.
Before I did any of that drilling, I'd soak it with break-free, etc. (machine oil) and wire brush the crankshaft as OGY was saying. Then thread in the 3/8-24 or whatever it is, to the PTO threads. Then I'd pick the engine up, and hold it by the clutch about six inches off of the floor, over some padding. Then I'd smack that PTO bolt head with my five pound hammer a few times, and watch the engine fall off, with the clutch in my hand.
You'd be surprised at how much ass you can give it, when using the engine as the counter weight to the hammer strikes. Or, you can attack it with an angle grinder and toss the clutch in the trash, but save the engine/crank.