Alternating Top and Bottom Invisalign Aligners?

i would not recommend wearing the trays for less than 22 hours per day if you want to achieve success.  Leaving the trays off for 12 or more hours virtually assures that the teeth will simply never truly be repositioned to the place they're supposed to be at the end of each tray.  Most patients experience less discomfort if they  wear the trays more time rather than less.  If you find wearing the trays unbearable perhaps you could try this alternating approach for the first tray only ... and once you're used to them wear them normally (22 hours per day) for two weeks.  This approach would not work for subsequent trays however, so before you progress to the second tray be sure you've adjusted to wearing Invisalign.

If there is a sub-clincial myofascial pain (TMJ) problem, it would not  be unusual to have your symptoms. I would recommend discontinuing the Invisalign and seek a definative diagnosis and therapy for the pain.  Good luck.