I personally have no info on whether these are fixed in other plugins, so I am posting the bug info I do have (pictures of the effects working correctly, any other info) so that these can be fixed in Jabo's plugin (or at least, become known bugs in the GameFAQ, which they are currently are not).
Glide64 works well with this game, but is often slow with the Mupen64+Glide64+Hacktarux wrapper combination even with my hardware. I also cannot get HWFBE working with the game.
I also know now that the Perfect Dark coronas (and in general, coronas in most N64 games) not showing is due to a depth buffer render bug. Gonetz has not fully solved this bug, yet.
...
Speaking of mempaks in another thread, I also discovered something very odd with the way PJ64 handles memory paks.
It sometimes generates redundant mpk saves even if the game made no use of the Controller Pak on the real system. Examples of games that do this:
1080 Snowboarding
Banjo-Tooie
Banjo-Kazooie
Conker's Bad Fur Day
Goldeneye 007
Jet Force Gemini.
I am 100% certain these games did not use the pak, as I own all these games, and have access to all the boxes, manuals and so on from these games. I deleted the mpk saves as a check, and they were regenerated as the game loaded in the emulator. I've also played these games extensively on the real system. There of course may also be others which I can't verify myself.
Normally, PJ64 does not generate mempaks when the game does not use them. It is only with these games that they are (and they should not be). It may even be bugs in these games, but I'll report it anyway as it may be a legit bug.