Why didn’t anyone tell me the reading order pagination wasn’t working? :-/
Well, it was kind of working – just seemed to cut out around page 27. I didn’t get it, until I realized that for the pagination it was only counting “posts” and not custom post types. Once I moved the call for the pagination to right below the query, it seemed to fix the problem. Except the header still doesn’t show on those extra few pages.
In any case, all the important information shows up so I’m not going to worry too much about that. Moving the query and pagenavi code is probably a temp fix though, since I’d prefer to have the pagenavi loading in the header so I don’t have to hard code it into each page.
I’m gonna hit up the wordpress forums and see if anyone knows what to do about the rest. Very frustrating weirdness.