Have you done fmq and ruler work before? umm...just trying to think. The aurifil thread is cross wound so it should be on the horizontal thread shaft with the thread coming off the top I believe, the Coats and clark I believe is straight wound so that should be on the vertical spool shaft. Do you have foam pads on the spool shafts also? Those make the threads unwind smoother I believe. With the ruler, make sure you are not pushing the ruler against the needle as that will deflect the needle slightly and throw the timing off a tad because of the needle deflection and that will cause a skipped stitch. I assume you do not have stitch regulator on your machine? You might want to try either slowing down how fast you are moving the fabric or speeding up your machine. If you are moving your fabric too fast and the machine is stitching too slowly, it may mean your needle does not have time to clear the fabric before it is moved too far away and the needle ends up getting deflected again causing a broken thread or a skipped stitch. similar, if you stop moving the fabric to think about where you are going, make sure you stop the machine too or it will stitch in place, make a knot and break. Again, I don't know if you have experience with fmq sorry if I am saying things you already know. It takes practice to fmq.
Do you have a ruler foot on the machine?