There's an existing, broadly used method for solving the line transition errors - you background color every two lines in an alternating set of colors. There used to be ribbon-feed printer paper pre-colored with this for certain applications that involve reading across lines a lot (like database output.) Seems like that is a more practical solution.
I'm not aware of eye tracking setups that are reasonably priced and that accurate, but I like the idea quite a bit :) I'll have to test it out some time - should be relatively fake-able by just moving a marker up/down with keys.
Here's what I mean: http://www.stationerytrade.com/upfile/images/big/20122221112...
What about using eye tracking? A device could just detect you're at the end of a line, and put a small marker at the start of the next line.