Mike, are you saying that the top pulley has the shaft extension as part of it, and the crankshaft ends inside the top pulley? If so, all is explained. You have to remove the pulley from the engine, and you can't do it with a puller because you are pulling and pushing against the same part: you can't push the shaft extension into the pulley hub, because they are a single component.
Can you clarify the status of the flat on the side of the pulley hub? Is there the head of a tapered pin in the center of the flat? There is usually a positive retention of the shaft extension piece if it has one, rather than relying on a press fit. A tapered pin would be a sensible way to do it, if combined with a key and keyway.
I suggest you don't try heating it up at this stage: you'll cook the crankshaft seal, and may distort the crankshaft.
If there is no positive retention device, you can probably remove the pulley by using a slide-hammer puller on the pulley instead of a screw-type puller. However this won't work if it has a pin through the pulley hub and crankshaft.
