Hmm. Everything you’ve described seems correct in the setup, and I haven’t found anything that points to what the problem might be. Let’s try a different approach.
First, please disconnect the EggBot from both power and USB, and then connect the USB cable (only) to it.
Here’s a very small test file:
Please open that in Inkscape, open Extensions > AxiDraw Control…, and select the first tab, called “Plot”, and then click Apply. Does that produce the same kind of communication error messages?
If you’d like to try this test with power, that’s fine too, but in the Timing tab of AxiDraw Control, change the top two numbers (writing/drawing and pen-up speeds) both to 1 (1% speed) first.