OK, not sure why what I'm describing doesn't match. I wrap my coils clockwise around the shaft of the Coil Master, and when the coil is installed with the legs on the bottom side of the coil, the legs end up the way I want them: in position to go under the right-hand side of the screws rather than being pulled in to the screws from the left-hand side of the screws.
The Coil Master, as Mike has said, is made for clockwise coils because the holes through which the wire is inserted are angled relative to each other to start in a clockwise direction.
That could be the problem then. And since your CM doesn't work that way... maybe hand coil, or a different type of winding tool.
But I think the critical part is the height above the air intake. So if you left the legs a tad long and with the tool still in it, work it down a bit, mounting the coil upside down shouldn't be a problem.