If my memory serves me correctly the multi-injector worked for Aidyn Chronicles, Banjo-Kazooie, and Custom Robo(if Im wrong, then I simply used the latest version of 64 Inject.) I had trouble with Hybrid Heaven(which I can confirm I used 64 inject successfully), Bomberman 64, Excitebike 64, Donkey Kong 64, and Harvest Moon 64 all gave me issues. I was able to run unpacked versions of all of them with Cemu as that was my main method of testing differnt settings and the zoom function.
As for the Mario 64 60FPS hack, neither injector will let me use the ROM(either version, though the widescreen hack crasehes while entering Hazy Maze Cave so it isn't recommended). I had success on my own manually injecting the files and running both though Cemu and Injectiine. While I'm no expert with this sort of thing I've spent a considerable amount of time researching the subject and could probably do a decent job making injects all on my own. My biggest roadblocks are making the making the images and the fact that no matter what I try I just can't seem to run NUSpacker due to yet unsolved issues with my computer. Fortunately your injectors solved both of these problems for me
Now I just need get the rest of these working and I'll be pretty content. At least with the N64 titles I have anyway.