Hey willus, thank you so much for your tool. 
I just discovered it and so far loving it. I'm using windows gui version for reading mostly academic papers and books. One quick question though. In native pdf output [-dev ko2 -wrap- -n -nt -90 -bp -c -col 1] highlights keep getting messed up. Tried figuring out what seems to be causing the problem using acro pro and abby. It seems at least in acro there are layers upon layers of text overlapped. Is there any way to fix that in the app itself or in the post-processing.
Another thing if there is already an TOC in form of bookmarks present in the input, then k2 outputs a TOC but it simply doesn't work. Is there any way to fix that as well?