I was still not able to do the V1.0.1 upgrade from POP but had an idea. I took the POP script and replaced the img files with the ones from v1.0 and they installed. I then was able to install v1.0.1 normally with the images written to all three controllers.
I now get a full boot but I still am stuck in a boot loop. The warning messages make me think I have a PLL chip or something not running at the correct frequency or something. I also don't get the missing files messages as the upgrade worked.
WARN: high: timing: sys_application TOOK TOO LONG: 605109us!
WARN: high: timing: sys_application TOOK TOO LONG: 698766us!
> WARN: high: timing: sys_application TOOK TOO LONG: 97262us!
> WARN: high: timing: sys_application TOOK TOO LONG: 146663us!
WARN: high: timing: sys_application TOOK TOO LONG: 26988us!
WARN: vm: No main function found. Will stop trying.
WARN: drive: no function with the name of emotion_eval: File or function is not found
WARN: high: timing: sys_drive TOOK TOO LONG: 27860us!
WARN: high: timing: sys_drive TOOK TOO LONG: 49976us!
WARN: high: timing: sys_drive TOOK TOO LONG: 41761us!
WARN: high: timing: sys_drive TOOK TOO LONG: 40314us!
WARN: high: timing: sys_drive TOOK TOO LONG: 523260us!
WARN: high: timing: sys_animation TOOK TOO LONG: 47672us!
This is the last set of messages before it reboots
NFO: vm: Loading fatigue_birthing(4012)
** bvr init: fatigue_birthing
** bvr main: fatigue_birthing
INFO: anim: Opened 0x304F[fat_birth_pre_pre] with 1 entries (1 properties each) at 8897.
INFO: anim: setting command to 12367 at 8898
INFO: plog: plogged id 12367, ts 8 @ 0x8006
INFO: anim: AnimSystem: find_entry returns entry 1 with weight 79
INFO: anim: Entry found in command fat_birth_pre_pre
INFO: anim: playing new Primary motion: 8260
INFO: low: motion: ts 8901: Load motion 8260
INFO: low: motion: Opened motion file birth_pre_pre
INFO: anim: playing motion birth_pre_pre[8260] as Primary at 8903
INFO: anim: full-body primary. stopping and disabling secondary and tertiary
INFO: low: motion: Set playback speed to 100% of normal.
INFO: plog: plogged id 8260, ts 8 @ 0x800A
WARN: high: timing: sys_animation TOOK TOO LONG: 47672us!
INFO: <0xff>
Boot info is
Pleo boot loader
7361 - Nov 15 2007 21:34:31
Starting image 8128 - Mar 19 2008 06:24:52<0xfa><break>
PleoPM version $Revision: 8139 $
INFO: high: setting monitor command to: stat power
Battery Voltage = 75, Min 75, Max 76 (tenths of a volt)
Battery Temperature = 0, Min 100, Max 0 (degrees C)
Battery Current = 264, Min 257, Max 335 (milliamperes)
Battery sensor value = 70 (% capacity remaining)
Battery sensor direct value = 70, Min 0, Max 70
Battery Voltage A/D = 667, Min 661, Max 669
Battery Temperature A/D = 875, Min 874, Max 877
Battery Current A/D = 37, Min 36, Max 47
Thermistor Resistance = 129938, Min 129785, Max 130291 (ohms)
Battery Internal Resistance = 0, Min 100000, Max 0 (milliohms)
Battery Capacity Consumed = 0 (mAh)
Powered up = true
RTK Adjustments = 0
RTK IK = 0
RTK VB = 0
Power monitor reset early warning = 0 (/LLO)
> WARN: high: timing: sys_application TOOK TOO LONG: 97262us!