Granted you’ve already start shooting, so it’s probably a little to modify your production workflow, but I’d highly recommend using animation specific software for your stop-motion piece.
Dragon Stop Motion is not terribly expensive https://www.dragonstopmotion.com/
Robot Chicken among other great stop motion productions use it. What’s nice about it also, is that will kick out your stills as quicktimes (and it will compensate whether you shot at 1s or 2s), plus you’ll still have access the raw images, in the event that you want to, say, bring the image sequences into After Effects for zooms, or rig removal.
Richard Sanchez
North Hollywood, CA
“We are the facilitators of our own creative evolution.” – Bill Hicks