Hi - thanks for your detailed description, really helpful.
The warning that the machine sends back is just a warning, it _will_ still attempt to draw the pixel, so it doesn't indicate that the command has been ignored or cancelled.
If the problem is that the pen isn't moving at all during width tests AND "render pixels", then I'd guess that it's not homed, or the motors aren't powered. You do still need to "set home" before you do any movements, to set the position, and to energise the motor coils (lock them). I've never used the ULN2003 drivers, so I don't know how they get energised.
You say that the machine works with moving the pen to points - you mean using the current firmware, you can do a "set home", followed by a series of "move pen to point" and "move direct" and it'll go there? That's a good sign.
Ignoring the fact that the width test doesn't move the pen at all, the way to "fix" the problem of having no detail is to increase the grid size and decrease the pen size. There's a page about it on the wiki that might be useful:
https://github.com/euphy/polargraph/wiki/Empty-pixels and http://www.polargraph.co.uk/2014/08/feedback-in-the-controller/
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