I agree that using a separate e-reader is best—I really enjoy the Kindle. I think they went through a lot of trouble to make it feel like reading a book (the “next” button is where you’l flip the pages, once you have a cover, you can fold it back for a similar “bookish” feel, the e-ink does not strain your eyes as much as a backlit thing would).
The e-ink eyestrain issue is actually pretty huge with me—I get migraines and become very light sensitive. Sometimes, when a migraine is in its early stages, if I get distracted enough I can ignore it. The computer is out for that since light = bad, but the e-reader or a book works just fine.
As for notes, there are several note taking systems in the various e-readers, but getting a cover with a notepad attached (like the Moleskin Kindle cover), would do the trick just as well (better, in my opinion). If you want to keep the location, the e-readers don’t have “pages” as such, but they do have a method of noting location in the text and you can easily jot that down as well.
If you are stuck with the computer, then play around with sizing and font/background colors if you can to see what works best for you. You might find that making it into a completely different experience works best because you no longer try to compare the two.