Hello! You are totally right- the yanfly message plugin was conflicting. The save issue has been solved.
It seems that when I switched to a different font, testers no longer had the issue, some it must have something to do with the scaling on Yesterday.
Here's a link to the game's free episode 1, but the OpenType font has not yet been applied to this build. If you'd like access to that, feel free to DM and I'll hook you up :)