DJ, I don't want to intrude into what went wrong, but it would be useful for you to think it through. At present it sounds as if you cut an internal thread in the engine-side clutch half by using a gear puller with a thread on the screw that was larger than 5/8" diameter. That would be a remarkably large gear puller - the biggest one I have only has a 5/8" thread. While I would not put it into a 5/8" bore, the marks it would make would be superficial unless the puller were off-center. It would be helpful if you posted pictures of the damaged clutch-half, partly to help other people in the future, and partly because we can then discuss whether it is really damaged so much that it has to be thrown away. Anyway, all of that is your business, but it would be a pity if you became disenchanted with gear pullers instead of working out what went wrong.

You seem to have said that you cut the other side of the clutch off rather than removing the three screws that hold the two halves of the clutch together. Again, I don't see why you would do that since it would be likely to damage at least one of the clutch halves.

I do not understand your description of the damage to the straight key from the crankshaft extension - a picture would be helpful. The "half-moon" you mentioned sounds like the Woodruff key that drives the clutch shaft, Item 111 in the illustrated parts list:
[Linked Image]

That item is Part Number 3802267. Please confirm that is the piece you were talking about.

Deejay can help you sort out what to do next, I am just asking for clarifications so that people who read this thread can follow what is happening and why it happened.