I think you are over thinking it. Like you, I don't think it happened when the flex plate broke.
I think the tranny was not mated flush when the bolt(s) were torqued. It looks like that broke while trying to draw up the tranny to the engine block, possibly before all of the bolts were in, perhaps trying to stab the alignment dowel pins.
The tranny will not flex with the rest of the bolts holding it in place.

 

I would replace the flex plate and bushing. Then try it out.

 

Alright thanks guys. I think I'm gonna have it welded after I get it out tonight. Just for peace of mind. You guys have helped put it at ease. New flexplate, bushing, and a fresh weld I think I'll be alright.

 

Well the Trans is out. Ended up wrestling it forward fard enough with my old man to be able to get the t case off. After looking at it I'm not sure I'm comfortable having it welded. Going to call around tomorrow and get some quotes on used transmissions, swaping out internals if I find a case, and purchasing a reman. I have a feeling a big bill is in my near future.