mgmueller, thanks for doing a detailed review. I do seem to do a fair bit of that "fumbling around" you mention (and it's not something I particularly enjoy) but with the amount of money I've managed to spend on ebooks it's definitely worth a little work to keep them safe from obsolescence.
Like you, my ebook experiences started on a Pocket PC in 2000. Without a lot of messing about with Calibre and Alf I'd be without half of my books by now.
Keeping everything in Calibre means I can buy any new gadget that comes along.