New Mac Pro: Setup/Migration Assistant never finishes

I am trying to transfer my existing (Early 2008) Mac Pro to a new (refurb) 2013 Mac Pro. I'm still in "setup assistant" mode.

The amount of information being transferred is about 120Gb. I've tried transferring over a direct-connected Ethernet from Mac-to-Mac, as well as a brand new Time Machine backup to an external SSD connected via a Thunderbolt 1 breakout box.

Every time I try to transfer, the transfer makes it to the applications stage in a reasonable amount of time. The progress bar is almost full. Then it starts doing the applications. At first, the screen shows "Transferring Applications"/"Transferring files to support applications" pretty fast. Then it starts getting slower. And slower. All the while, the completion time (which was "about a minute" starts creeping up.) The first time I let it run all night. By morning it was saying there would be over 250 hours to completion.

I've tried it 4 times since then (including a complete system reinstall), and the same thing happens every time.

I feel like I'm down to 2 scenarios:

1. 
   

   The Mac Pro has a hardware issue. I've already run the hardware diagnostics, but nothing shows up. That being said, this is a refurb, it's possible something is wrong that only affects the new machine during long transfers.

   
   


2. 
   

   There's something in the backup or my applications setup that's causing the migration to get stuck in a loop. I've looked on the system drive for a log, but I haven't found one.

   
   

Here's where it gets really, really bizarre: I can't find any sign of the files transferred on the new Mac after I've stopped it. Not a single file appears on "Macintosh HD" on the new Mac.

Any ideas? Apple can't help me in the store until Monday, so I thought I'd ask here.