The keyboard design was a failure
I had wrist ache last thursday, and had to return to the original ergodox setup. 11 days were enough to cause very credible uncomfort.
Proper RSI would trigger with lot of normal day activities, so mine isn't too severe. It will heal when I reduce typing for a moment and let it rest. I have lot of alternative activities in a backburner so it is not a problem.
There are many possible culprits why my makeshift ergonomic keyboard design was so effective at causing issues ergonomy usually attempts to reduce.
One possible culprit is that the extra rows in the keyboard require me to reach too far. The frame isn't curved enough to give access to them.
Another possible culprit is the tilt. In ordinary keyboard your wrist is twisted, but the palm rests on a table since the keyboard is aligned with the table and is oriented low enough to allow arms to take support from the table plane. The table under your hands may be an ergonomy increasing factor.
Third possible culprit are the tilted keys. The tilted keys may require much more effort to press. I think this is unlikely but could explain the problems.
Fourth possible culprit is the ergonomic rest floating apart from the keyboard. My ergodox keyboard also slides on the table and that makes it bit more unfomfortable than it could be. This is a possibility.
Fifth possible culprit is the new improved wrist rest. I may have designed it with the intent to have the arm hang on it during typing! This may cause it to form an additional surface that builds up friction on my arms.
Sixth possible culprit is actually the ESC key. It may be the position is wrong in the first place and causes constant strain to my left hand, making it strain more than my right hand, making it much more sensitive for injuries. I may have to move the ESC key down to the caps lock position to anticipate this.
I will improve the design to take all these potential problems into account and provide some adjustability, things I can easily make adjustable would be different keyboard tilt angles. And I can add a way to attach the wrist rest to the keyboard so they don't move in respect to each other.
If I won't manage to make an ergonomic keyboard, I still have a backup plan! I can still make a flat ergodox-like keyboard from the parts I have. Just some slight changes to the layout can matter.