If you limit yourself to e-ink readers, I predict that you will suffer from endless problems with finding software that does what you want. You may have to bite the bullet and get a general-purpose tablet PC.
Go for a lightweight tablet with a Wacom stylus (digitizer), as this kind of stylus will give you a far better user experience for highlighting and handwriting than an ordinary capacitive stylus would. The Surface Pro has a Wacom stylus, but is too heavy for comfortable one-handed use. I would recommend looking into the Samsung Galaxy Note Tablet (running Android), or the Samsung Ativ or Thinkpad tablets (running Windows 8).
In the Windows world, Qiqqa is a cloud-synced reference and citation manager that will sync annotations, although you can't export the altered document like you wanted. It's likely that both Windows 8 and Android have numerous PDF annotation applications which will suit your needs. You may have better luck in the Windows than the Android world, because you will want your application to have native Wacom digitizer support (distinguishing between finger and pen presses, allowing you to scroll with your finger and highlight with your pen). There may be a PDF annotation application in Android that does this, but Wacom digitizers have historically been far more common in Windows than Android, and the good Wacom support in Windows applications reflects this.