My son does cheer and I've had a bit of experience doing his events. I usually use my 35-100 f2 and have it set between f2 and f2.8 depending on the light. Also usually ISO 1600 and keep the shutter speed above 1/500 for the older teams (middle and high school). Above 1/1000 would be ideal, but that hasn't happened at an indoor event yet. With your settings, you must have been in worse light than I am used to from events.
My suggestion with camera settings: Get off of auto ISO. It seems to want to lower that before it raises shutter speed (I see pics with ISO as low as 640), and that isn't what you want. If ISO 2000 is not too noisy, go with that. See if that doesn't raise your shutter speed with leaving the rest of the settings the same.
Second: Please reconsider using flash - don't do it. The last thing you want to do is distract a flyer or a base as they are doing a basket toss. I know you will get raccoon eyes and the like because of that, but it is better than a fall.
Third: Your framing is pretty good. I would like to see some "Team" pictures of everyone being in sync during a tumbling pass or something like that. You have a good handle on getting an individual during the action, but I think your timing is a bit off. Most of the action type shots are just a split second away from being ideal action stoppage (eg:
A Chance Encounter | Cheer )