Woke up to let the puppy out. I'll try to answer all questions quickly.

I do not know what the runout was on it either time. Sometimes they tell you to trim the input if you have a certain bearing in the crank, can't think off the top of my head. But that is what the transmission guys will say (mopar specific guys). It did not change anything, so they replaced that completely.
I don't remember what I meant when I said it looked sideways. I probably just didn't know what I was looking at, at the time haha. That was probably about the time I overhauled my first transmission on my car. If anything, I'd imagine we replaced the transmission mount. Pretty sure even twice. We were literally trying everything, multiple times (where is banging head against wall smiley)
I will check the bell-housing to front bearing retainer. Would hope its the same as we got the trans overhauled and bell-housing from the same person. Thanks!
CabBurge, never wrecked and the vibration felt would be sitting still or driving above, say, 3000 rpm's. With the clutch pressed in or out.

I'll take pictures of everything as we take it out.