Arduino blocks i2c bus

Yet if you look carefully at your dropbox picture of how things were actually wired, you have a red power wire going from the breadboard to the 5V pin of your UNOr3 (the one in the upper right of the picture). I'm not sure how you didn't release the magic smoke with twice the voltage..

Look again, the one with the USB plugged in is the source unit. The red wire is coming from the +5V of the source unit to the Vin
of the second UNO, meaning that the regulator on the second unit only has 5V on it's input instead of at least 7V so the second unit (with the +5V connected to it's Vin) is running off about 3V. (as opposed to a higher voltage as suggested).No damage possible in this scenario, but second unit would probably not function reliably.

I guess the next question is, could this cause some sort of memory buffer shrinking causing the Arduino to lock up the bus when it was under powered?

It should be assumed that the unit could not be expected to work properly under those circumstances so all your observations are
pretty much useless if they were made during that scenario.

True. I would make new ones, but my Pi is sort of dead, which I suppose is probably related somehow, but that's for a different forum.
Thanks for the help, everyone. Is it customary to close threads here?

Do you know how to write diagnostic programs for the Pi ? With an arduino we usually start with Blink example and then expand from there. The wiring we spoke of does not explain any issues with the Pi.

And no, we don't "CLOSE" threads. We just go away and forget about it and leave the post as is for others to learn from :
ie:
Moral of the story ?
CHECK YOUR WIRING TWICE !
but you know that now...

The code I'm running on the Pi is basically blink, just the LEDs are attached to the Pi through 2 Arduinos and 16 TLC chips, and there are 240 of them to blink. The issue with the Pi doubtfully related to the Arduino issue, and more probably related to my paltry wire-plugging skills.

Can you disconnect it from the TLCs and run blink on Pi outputs only ?

Yes, I know how. No, I can't because the Pi won't boot. No lights or anything. I think the big capacitor by the USB plug is dead or something.

sorry to hear that. you can buy an ATmega328 chip with OPTIBOOT bootloader for $3 from DIP MICRO. You need the 18pF caps as well . You will also need an FTDI breakout to upload sketches

This is cheaper than the FTDI BASIC from Sparkfun but works the same.
You can breadboard the uC chip ,
http://arduino.cc/en/Main/Standalone and be back in business in no time.
PS- BUY SEVERAL ATMEGA328s

OK, thanks!