Before you overclock and add heatsinks, please refer to Twitch0815's post and note the line about plugin.
N64 games run better or worse depending on the video plugin selected for Mupen64Plus. Since you didn't mention this, I suggest you start there. Try all video plugins for Donkey Kong, and choose whichever one seems to run the best. Also, the standalone Mupen64Plus has better performance (non LR version).
Look here: https://www.reddit.com/r/RetroPie/comments/3dqcs6/retropie_n64_compatibility_list_rpi275_tested/
It says Donkey Kong 64 works best with the rice video plugin, and there is no mention of slowdown with a non overclocked RPi.
Finally, yes, use a power source with the recommended amps. Mine is 2.4 amps. The RPi3 needs more amperage than previous models.