It sounds like you did not have the torque convertor properly seated into the trans. With all the pressure you have put on the torque converter, you may have damaged the trans front pump.
You do need to remove the TQ and see if trans and engine block now match up, as noted on the prior post. If it does, you should have a trans shop check the front pump and and TQ to make sure you didn't damage them. If you don't, you may be taking things apart again for a trans repair.
When the torque converter is installed on the trans, it needs to be spun to make sure that it seats into the front pump keyway. If you don't get it seated in, it will stick out too far and cause things to not line up as you have discovered.
The broken part of the bell housing would probably be best repaired by aluminum welding.
