Re "Wake up foggy headed? Clear your head with with the kapha mantra hoom though if you really want to clear it try the Ganesh mantra: om gam ganapataye namaha. Upset stomach? Use the pitta mantra. Constipation? Try the vata mantra.":
We were always taught that during TM we should allow the mantra to change its "sound" and not interfere. Sometimes it can even be just a pulse; sometimes even just a modulation of other thoughts that flit through the mind; sometimes just the ghost of a sound . . . I'm sure if someone told me to repeat "om gam ganapataye namaha" I could manage it but it would keep my consciousness at a surface level and block any move towards transcending. Do you find picking up other mantras and using them as your "focus" is straightforward and unproblematic?