I have managed to fix the "490 Tools Position Check" error. I can't tell exactly what fixed it, but the codes I did put in was "T504M7" for the tool that was in the spindle at the time the error came.
Anyways, even though I had already tried that a million times, it fixed the error.
The only other one we're having is the drilling head, and it will not retract certain bits at different times. Like I said it's totally random to what bit it will not retract. Which makes its so hard to figure out because we can't get one bit to focus on.
At times I may issue the M111 code to retract all bits, and it may work, but leave 1,2, or 3 of 5 bits down. Yet it may leave all bits down and 30 seconds later it will retract them.
One thing that has worked is; on top of the drill head there is black plug like blocks, 1 per bit, and the top of the block has a breather screw on cap. If there is a bit that is stuck, we take of the cap, and put our finger over the hole for a second. You can then hear a little air suction and it will retract the bits.