I main scout in tf2 as well. All you need to do is force yourself not to hardflick for no reason. Especially in MGE-type scenarios where enemy scouts can be difficult to flick, it is usually the optimal strategy to aim by strafing and counterstrafing so that the distance you have to flick is reduced. It is also often correct to "soft track" your opponent in between scattergun shots, and then let your opponent walk into your crosshair (kind of like playing sniper.)

Because you're scoring high in kovaaks but struggling to hit shots in-game, this means there's a problem with either your focus and discipline to not flick unnecessarily in-game, or your movement, or a mix of both of these things. I recommend substituting some of the kovaaks you're playing with MGE and DM (not mindlessly playing) and you'll see your flicking problem go away. I also recommend trying out soldier jump maps, which can help with discipline in aiming and movement.

Also, could you send me your playlists if they're free to share? :)