If I remember correctly you can't get to the upper most bolt until you drop the back of the trans and the motor swings down. You do have an LS1 though! So your engine/ trans may be set back a little more than mine. In your case it might be easier to leave the bellhousing on the motor. But don't freak out, for problems there are only solutions.
We'll get it out. I have ratcheting wrenches, they fit into very tight spaces.
How do you know that the internals are damaged BTW?