I understand that you mentioned the hood will be properly attached, but that should be where most of the issue is. Also try to use white lithium grease on the gears to help make it easier to spin. Your wheel should be able to freespin for 5-7 seconds for it to have minimal friction.
IMO, we had ran a 3m 1:25 HS flywheel before and have had the same issue that you had, disregarding the hood. Once we moved down to 3m 1:15 turbo, it drastically improved the firing range and force applied on the balls since it has more torque compared to 1:25. Another tip would be to entirely take off the antislip on your hood. Main point being that antislip promotes backspin, increasing accuracy yet drastically reducing speed. Taking it off will transfer more energy to the ball to move it forwards, giving it enough force to toggle flags.