I had similar problem as you when installing the ballscrews. What I did was move the X axis table all the way to the left until the end of the ballnut touches the cncfusion block. I didn't have to file the X2 table but only turned the ballnut slightly so the return tube is clear of the side of the table. I turned it down facing.
Then again all x2 aren't made the same so I guess yours may need to be slightly modified to accept the ballnut and ballnut mount. What driver, PSU and stepper motor you are using?
I am using 150W 24V 5A keling PSU with KL5056 drivers and 495oz.in motor. I am upgrading to 500W 48V 10.5A power unit from ebay. Its a good deal cheaper even with shipping. 24V is just not enough for my X2 mill.