For posterity:
The problem ended up being the wireless card.
The Fit-PC2i has a Ralink wireless card taped to the motherboard where a PCI-E card would normally go, but it's connected to a small USB header. To even see it you have to completely disassemble the machine.
After getting underneath the motherboard I disconnected the USB wifi card and installed an Atheros card in the PCI-E slot. It booted up fine.
It's it's any help for debugging for devs, it was the RT2870 ver. 0.33 driver causing the crash. The wireless card was working fine in the current Gentoo installer kernel and current kernel.