If you use a Retroarch emulator, with any core, your run will not be accepted.

As exposed by @garadas21, Retroarch lag reduction is deliberately making the emulation less accurate, in order to make it play faster.

There are a number of other emulators that are accurate. Please use those instead. Examples: Nestopia, Fceux, Mesen, Higan, or OpenEmu with one of the above cores.

How about the core on the MiSTer?

I don't think the Retroarch rule is valid any longer, FYI. It is not an emulator itself, one can run FCEUX etc within Retroarch. Many speedrunning communities have done away with this rule as I understand it. Correct me if I'm wrong though!

and fwiw MiSTer should be fine IMO as it's about as accurate as you can get outside actual hardware.

Sounds good to me!