How do we get this updated in RetroPie?

parallel doesn't replace glupen at all. parallel is the new name for lr-mupen64plus (which you weren't previously using). lr-mupen64plus is now a fork of glupen. your saves should work on that. @jdrassa 's link explains all.

@loganmc10 Sorry I wasn't very clear, I have framebuffer off currently. I turned it on, and then I turned it off. There's a noticeable graphical difference, so I know it's definitely off, but somehow the pause delay is still gone. Framebuffer On does increase the lag even worse though. But even before I messed with the framebuffer, there was input lag is what I was trying to say. I don't think there's a fix though, it's just how it's currently coded it seems.

paging @BuZz :)