My Juki is really sensitive to lint buildup. If I don't keep the bobbin area really clean it messes up the tension. Mine has fmq'ed on everything and the only real problem I had was when i was trying to quilt a heavy T shirt quilt with French Fuse interfacing behind the shirts. The only solution I found was to use a topstitching needle. They have a longer eye and so they don't skip sts like the regular needles were doing.
Try your fmq with your feed dogs UP, and less pressure on the pressure foot. That works really well on my Juki-- helps me to make more even sts.
Also your 'micro sts' sound like the the quilt got stuck in some spots-- maybe where it was thick from seam allowances? The feed dogs up will help keep moving the quilt along as you fmq.