Hi SP777,
not forgotten! but we will probably need to clean up the reader interface so we can tackle the overlaps and the scrollbars. I'm sorry, but this will probably be done after next release (which we're currently preparing).
As for writing annotations/highlighting into the PDF: I know the general procedure for that. However, I'm not really aware of a feasible solution that would run on the Kindle itself. Basically, that is because I only know of iText as a reliable library to do such things. Unfortunately, iText is Java based. However, I think it would be easy to create a _Desktop_ application that could do that task. I'll see if maybe the cvm on the Kindle is up for the task, but I doubt that old Java version will cope with iText. Also, I might have to look into libpodofo, it might have evolved and maybe it can do it, too. However, this will take a bit of time, too.
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