So I pulled the pan and found bearing material in it. I then pulled all the pistons and the rod bearings (Clevite 77) looked good on all except one that had the bearing material go through it. I then removed the mains and crank and found the back side of the thrust bearing worn and burnt.
This is the front side and what the back side should look like.
I know what caused this but didn't know it was an issue. When we were lining up the trans and engine I had a hard time getting them to go together. I finally was able to push them together enough that both dowel pins were in. Adam was helping and said that they had the same issue with the 351 and had to use the bolts to pull it together so we did the same. Once we got the bolts in I was able to shake the engine and trans together some more so I didn't think anything of it. However, after seeing the crank it was obviously a clearance issue. So I measured everything and found that the pilot bearing is about 1/8 inch too far out. I did some research and found that this is an issue when using a 400 bell housing with a 429. I don't know what the bell housing came off of but Andy said something about it being from a Bronco. In my research I found that the Bronco came with a 400 and I assume that's what this is from. I also found that there are two different pilot bearings and again I'm assuming but the other one which is smaller goes further into the crank must be what we need.
I'm waiting to hear back from Andy to see what he wants to do but I think the crank is wasted but he'll need to take it to a machine shop to have it checked out. This really sucks!
Here's the crank.
I guess the only good thing I have to say is that at least the block is standard bore and still has the factory pistons. Also, the crank (if it's salvageable) has never been turned.