[EndlessAzure]

Not sure what to tell you. Damaging the engine is obviously a bad thing to do. Images would help a lot. You can already see the damage from the missing piece of engine. With regard to the bolt that's not seating fully, I'm going to gander that you likely stripped out the threads of the engine block.
- The missing material may or may not matter. It might take time, effort, and possibly some money to fix the bung threads on the engine block. Would consult an experienced mechanic on it.


Forcing a transmission on could mean many things. You could also have pushed the pilot bearing out of the flywheel if things were misaligned enough. If you missed an alignment pin, then the transmission may not have not been fully clocked in and seated. The bell housing should be flat against the engine once everything is seated. All the bolts should thread on easy and the bell housing should draw toward the engine without too much effort.


The mistake most people make when working on the transmission was that they did not support the front of the engine. When you take the transmission out, the engine has no rear support and flops forward. This means the flywheel side is pointing slightly upward. When you work with the transmission from underneath, it's only practical for the transmission to be straight-and-level or pointing slightly downward. That means they are hopelessly misaligned. You'll have to rely on a lot of luck to get them back into alignment without this knowledge, or some help with getting the engine back to level.