I got the TX1 board running off of a second VRM using
option #1 from this post on the nvidia forums. They warn about the hard shutdown being possibly an issue, but the board seems to be powering on fine for now.
Haven't tried connecting to it yet after a few startup/shutdown cycles or driving around, as we ran out of time in the lab.
Marshall, did you try Option #1 before moving to Option #2 for changing the capacitor values? We didn't have any capacitors on hand that were the right value, let alone size. Also, could you provide more info on the supercap you guys are using?