I am not Synthetos, just a Forum lurker/moderator. I do see the requests to the Contact URL, I can't recall if I saw yours or not. When did you send in your query?
Some background that might help:
The thread you referenced that started way back in 2014 had origin in a Lock Bit setting that was blocking flashing of the device, IIRC. Unless you have a very old tinyG, that is not likely your issue.
In late Dec 2015, a small batch of tinyGs were factory programmed incorrectly (again, fuse or lock bit programming) that made the tinyG overly protective of low VCC voltage, resulting in self destruct that corrupted both the tinyG FW and the bootloader FW. The recent references you post above, about how to use the MKII to reflash, are aimed at that firefight.
You obviously have a functioning bootloader, based on your terminal logs above.
What version of SPJS do you have loaded on your Pi2B?
OK, so you are a linux guy (me openSUSE), I wanted to know your Desktop OS so I could point you down the correct path for bypassing SPJS and using avrdude from the command line. You already figured that out.
I am a bit stumped
Your flash log looks OK, except of course for the verification error.
For the moment, I am fixated on your avrdude version 6.2-5.
Where did you get that from?
My openSUSE has avrdude 6.1 in the repositories. Works OK directly from desktop.
Chilipepper is actually using avrdude 6.0.1 in the SPJS implementation.
I vaguely recall downloading an avrdude version 6.2.something at one time, which did not work with tinyG. That could be your issue.
Here is a wild guess as to what may have happened when binary data got sent down as Gcode:
In addition to the user parameters you see with $$ command, there are other parameters in the EEPROM that are used by tinyG internals. Something in the command stream may have caused tinyG to corrupt EEPROM, then crash. The best way to fix that corruption is to relaod FW, which rebuilds EEPROM parameters as part of the install process.
I am actually somewhat surprised the bad command stream ever got sent - the ChiliPeppr Gcode widget and SPJS are very Gcode knowledgeable. Hard to predict how your binary file got interpreted.
See if you can find an avrdude 6.1 for your Ubuntu system and try that