My pdf pages are 2.75 x 4.25 (as suggested above) but there still appears to be some misalignment in the zine..
This does happen sometimes, even when the pages are measured out to the right size. And I'm afraid I haven't been able to find whether it's a bug that I could easily fix, or if it's just a limitation of how Zine Arranger currently does the layouts. I'm suspecting the latter.
Whenever I do another big update, I plan to look into a using whole different approach which should let it get more precise, but that's going to require quite an overhaul. For now it's just probably going to end up a little wonky sometimes, though hopefully it won't be too terribly noticeable once the zine is folded.