I had the same thing happen to the pilot bearing when i was helping a buddy removing his. We fought with the damn thing forever with just the puller with no success. See if any other parts stores like napa, pep boys, autozone, or advanced have a pilot bearing puller that attaches to a slide hammer and it should pop right out, at least it did for us. 3 hits with the hammer and it was out laying on the ground.
Here is a pic of what it looks like