I think you need to get under 11.30 seconds to get perfect score (I got 998 points from 11.35 seconds).
It's a good idea to hold the joy-con like you would hold a frying pan, at the bottom of the controller. Short flicks is good to save time, but only do it when you know the cube will land on a raw side. I did a couple of hard flicks so the cube will turn over completely, which is good since it makes it easier to land on a raw side the next flick you do.
Holding the joy-con slightly slanted to the side will make it spin around, which means you mostly only need to focus on flicking.
I feel it's better to focus on getting the cube to land on a raw side with every flick, rather than waiting for the cube to turn around and do a short flick.
Arrowstotle did a good job explaining how to handle the joy-con, check him out: 
There is no real right way to get 1,000 points in this game. You simply have to play it a few times and get a feel for how the controls and physics are. Also rumble is super helpful so you know when you are done.
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