Well, the root of your problem is that you switched away from vulkan, which utilizes the highly-accurate ParaLLEl-RDP to OpenGL, which uses extremely old and inaccurate (but also very fast) Glide64 RDP plugin.
If you use mupen64plus-next with the “gl” driver, it uses the better-than-Glide64-but-still-inaccurate GLideN64 plugin.
You’ll have to find some combination of core and RDP/RSP plugins/settings that runs acceptably on your system while still maintaining enough accuracy to run the game(s) without noticeable bugs.
if your system can handle it, mupen64plus-next with the vulkan video driver and ParaLLEl-RDP and -RSP is your best bet for accuracy plus performance.