... first and biggest problem is that was an offset closet flange because the dimnsion off the wall was not correct ... you could have used an inside closet flange if it was roughed in 4" but it appears it was 3" and inside closet flanges on 3" usually cause the toilet not to flush good ... so not that you have hacked it off ... your only option could ahve been and its a risky one is to use the tool that removes the socket from inside the hub of the pvc fitting ... but you used a 3" street 90 belew the slab so that option is out .. now you need to surgically remove the flange hub from the outside and try to break it away with a screw driver ... i say chop it up and fix it right and while your at it ... rough it in to 12" off the wall this time.
Thanks for the detailed reply.. I think I understand what you mean, but it sounds like you are saying the proper fix involves ripping up the concrete and doing more specialty plumbing or that I would need another set of hands for.

I can handle lots of diy around the house handy[wo]man tasks, but this might be too much. I got an internal pipe cutter (wish I had know about this a month ago..) to hopefully carefully remove the 3 in. offset flange.Just in case so I wouldn't have to keep running to HD, I got:
a 3'' x 3' pipe ( in case I need a few extra inches)
a connector/female on both ends/coupler
a 3'' plastic flange
a 4'' flange (didn't know size of waste pipe until I removed the offset)
a 4'' to 3'' offset flange - same one as the original.. just in case there was a reason they did it that way as much as it sucked.
going to work on it now.. wish luck..
one more question, my dad just got a dual flush comfort height elongated toilet from lowes. install has gone well so far, but when I placed the gasket on the bottom of the tank before I put onto the bowl, it felt like there was a large sponge that wasn't compressing. I'm pretty sure the gasket is right side up..