Electrical – Resistors in serial communcation

Whenever I've gotten the 'not in sync' error, it was related to my just missing the reset timing (or forgetting the reset entirely!). For my breadboard, and Eclipse/AVRDude, un-grounding the reset pin just before or at the same time as I click the upload button is the right timing. But also check that your PC really does see the adapter when you plug it in.

Later arduino boards are built to reset whenever a serial connection gets made, and programmatically by the bootloader. This blog article describes how it works, and even more interestingly, how to hack it onto earlier boards. It shouldn't be too hard to put it on a breadboard if you wanted to. The chip needs to have a compatible bootloader, of course (which you've already put into yours). For breadboards, I just do the reset-button / mouse-click dance.

Those 2 lines are probably not related

My guess is that these two lines aren't a serial "data" bus at all, given that it's really unlikely that the data line would be sampled on both clock edges. At least, they aren't part of the same communication scheme.

The clock-like trace is likely the "step" command. It's purpose is to inform the ink carriage motherboard that the stepper motor has stepped the carriage to the next position across the page.

Some alternatives?

The data-like trace is possibly a limit switch or other sensor of some kind that indicates home position, beginning of row, end of row, etc.

Or alternatively, it might be an asynchronous (no transferred clock signal) serial data link. The long idle periods between bytes might be necessary to prevent inter-symbol interference and promote clock-recovery.