So another thing we noticed probably missing is the little shield piece that bolts in where the motor and the transmission connect, I think its called the dust cover or something similar? Is this something else I will be finding at a junkyard?

And assuming anyone knows what I am talking about, how easy is it to put back on? I'm hoping it wasn't something that needs to be put in with the motor out.

 

If you're talking about the transmission access cover then you should be able to find one at the junkyard. I don't remember for sure, but I'm pretty sure that it should go on without having to unbolt the transmission (if that isn't the case clipping the one corner off will let it go on without unbolting the transmission.) You will need to remove the starter though (2 bolts). Make sure you grab the 3 or 4 little bolts that hold the cover on too since you're most likely missing them.