Over the years I've looked at a bunch of readers for CBZ/CBRs (I liked
Comic Zeal the best of those), but including all the books that I've scanned myself, comics and otherwise, I've found that the Japanese app
iBunkoHD fits all my needs the best. It can handle left- and right-bindings, bump the 2-page spreads left or right a page to compensate for wonky pagination, and is overall quite nifty.
So PDF it is. I'm just trying to find a way to make the conversion process more streamlined.