Tharden,
I agree that a rider can make a huge difference, BUT, there is NOT a 250 2 stroke that can hang with a 500 (red, green or orange) that is running properly (& geared correctly). I have a 250 drag bike that is pretty quick (it will run any 250 with just a pipe & reeds) & my STOCK K5 will MPH it in 300'. The 250 is lowered etc for this & the 500 is not so the 250 is quicker because of this, but if you add another 100' it is all over, the K5 ( or red or orange) will go by. I haven ridden 250's most of my life and they have plenty of power for most all situations, but if you drag a 500, and you get into 3rd gear the 500 is gone, I know this as my buddies had the CR500's and we would practice our starts from the gate on a MX track every week & it happens just like I mentioned.
Now let's try to get you whipping up on ALL 250's. Think of John Force running a 10.5 slick, his times would not be there as he is just spinning his tires, it sounds you are doing the same with the current gearing you have (adding teeth to rear is a torque multiplier) as the motor is over powering the traction available, digging a trench, not moving forward. Now take away some of that torque and spread it out longer you will obtain forward motion longer between gears. Try a 15 tooth counter shaft ( it's in expensive) to confirm you are on the right path & let us Know.