@KillDozerX a Pi2 is likely to struggle with N64 emulation. However, as @dankcushions said above, why are you installing 4.1, the base install is on 4.2.3 (possibly higher by now)?

When I referenced the https://retropie.org.uk/forum/topic/3/read-this-first link, you really should have followed it. Try completing the requested information (requested in that page):

Pi Model or other hardware: (B, B+, 2 B, 3, X86 PC etc..)
Power Supply used: (If using a Pi)
RetroPie Version Used (eg 3.6, 3.8.1, 4.1 - do not write latest):
Built From: (Pre made SD Image on RetroPie website, Berryboot, or on top of existing OS etc.. - please provide the filename of any image used)
USB Devices connected:
Controller used:
Error messages received:
Log found in /dev/shm/runcommand.log (if relevant):
Guide used: (Mention if you followed a guide)
File: (File with issue - with FULL path)
Emulator: (Name of emulator - if applicable)
Attachment of config files: (PLEASE USE PASTEBIN.COM FOR LARGE LOGS)
How to replicate the problem:

@Capt_MorganCreek thank you very much

@loganmc10

Sorry I wasn't very clear, I have framebuffer off currently. I turned it on, and then I turned it off. There's a noticeable graphical difference, so I know it's definitely off, but somehow the pause delay is still gone. Framebuffer On does increase the lag even worse though.

But even before I messed with the framebuffer, there was input lag is what I was trying to say.

I don't think there's a fix though, it's just how it's currently coded it seems.

Please update retropie setup and do a source based installation again.

@loganmc10 I added it for both X86/X86_64 anyway (keeps logic simple).

@Finndersen should be in /opt/retropie/configs/all/retroarch-core-options.cfg

Perhaps the .sra file is made by one emulator and .srm by the other..I'll have to check tomorrow