I hope I'm not too late. For now, do nothing.
First of all let's talk about the necessary and possible modifications.
This v1 Dock with Omega2 project is a lot of work... it may not be worth it.
Electronic circuits DIY and soldering practice are needed.
You have a version 1 Arduino Dock. Please let me know:
What is the SMD marking code of the power supply IC?
The MCU is an ATMEGA328P AU isn't it?
Huzzah! It works now! I think a problem I was having was that i was using an older version of the Arduino IDE, and then I upgraded to 1.6.10 which was giving me issues regarding the uno.upload.via_ssh=true line. But now that I installed 1.6.6, I got it to upload normally.
I assume that the omega does not get (enough) power from the Arduino dock. Any ideas?
Did you try out other USB-cables?
Also try to connect a USB connector direct on Mainboard if you use a Desktop computer with a front-controller. As longer and older the cables are, bigger is the possibility to get power loss.
@Anco-van-der-Kolk I will be writing the library in C/C++
While I am far from being an expert in Python, I believe the bulk of my library will be callable from Python just as is done with the current code for Neopixel control.
Though I have no idea as to how the interrupt from the Arduino to the Omega could be handled in Python - sorry
Regarding using a resistor bridge for change from 5v to 3.3v - yes, since the signal is only needed one way (Arduino -> Omega), this would be feasible if it is really needed.
Two suitably chosen resistors in series - one end to GND the other end to the Arduiono pin and the mid-point to the Omega pin
@Will-Kostelecky Yep, you can program the dock through the ICSP connector just like any Arduino.
From what you're describing though, it seems like you might have overwritten the Arduino Dock's bootloader. Try going through the steps in the Arduino Dock Initial Setup article to flash the bootloader and then try flashing a sketch.
EDIT: @Kit-Bishop can you please add resolved to the topic title and add the tag resolved to the post? thanks!