I was able to convert my .srm save file from lr-mupen64plus-next to an .sra file with this online tool.
https://drehren.github.io/ramp64-convert-web/
I then copied the .sra file into /opt/retropie/configs/n64/mupen64plus/save/
Then I launched ocarina of time with mupen64plus-GLideN64 and played it nonstop for about 2 hours without any crashes or major issues. GLideN64 may have had a few more video glitches than lr-mupen64plus-next was having, but not a single crash for that entire period of time, and that was picking up the game where I left off playing with lr-mupen64plus-next.
So it seems that I don't have these crashes with standalone emulators, but do with libretro emulators.