What are your settings for m64p for the cxd4 rsp and sdl2 audio? I can't seem to get rid of intermittent audio popping even in games like Ocarina of Time which are easy to run at full speed. I have the buffer size at 2048 but it still happens. I tried it in parallel with angrylion and the audio was fine; it even runs at around 120fps unthrottled.
Well to be honest I haven't touched the sound settings in m64p, and either my hearing is bad or I'm just lucky because I don't hear any audio popping at all with default settings in any game.
As for cxd4 the only thing I have changed is the DisplayListToGraphics option enable for angrylion to run.
A side note, I tested the latest public release of GLideN64 (4.0) today in both m64p and Project64 and I enabled all the options to make it as accurate to the N64 as possible.
Well the result was quite good for 14 of the 15 games I have, only BioHazard 2 was really bad and the water in the Frigate level in GoldenEye looked bad.
I'm starting to wonder if N64 emulation is cursed somehow, because right when you think that you have found something that could be good, one little thing pops up and it's all back to square one again.
m64p with angrylion, cxd4, cached_interpreter and vertical sync enabled still seems to be the best combo at the moment.
I haven't given up on Project64 though, still a fantastic emulator with great options.