In Grease Pencil I added a video reference clip to draw over and added the audio from the same clip, but they are out of sync. The video runs super slow. I tried running it several times to allow it to compile in memory but… still slow.
Does it matter that it is an MP4? Should it be a .mov?
When it is playing the frame rate in the upper left says it is running around 17fps but the clip is 30fps.
Any fix?
Hello there 
Try going going into the Playback options (Timeline workspace) and check for Audio Scrubbing and AV Sync.
In that Panel you should be able to find all the Option you need to adjust the viewport FPS.
Tell me if this solve your problem
Hello
mp4, mov, qt , webm, mkv, avi are just containers.
Your video inside is most likely compressed by AVC1 (Advanced Video Coding) or VP9 (video on YouTube is encoded in this codec). also audio can be encoded in different codecs in these containers.
There are codecs for playback only, they compress the stream well with good quality, resulting in a small file size. But they are not suitable for fast rewinding or editing, because they take a long time to unpack.
And there are codecs specifically for editing - MJPEG, DNxHD, DNxHR, Apple ProRes…
You need to transcode your video to MJPEG or DNxHD. Then it will not slow down in the blender.
You can try inserting your video into VSE in blender and generate a 100% proxy for it. The blender just encodes the proxy for video tracks in MJPEG.