A while back a question was reised if it would be possible to have an open type font that would make these distinction automaticly.
I have developed a font that works 99.9% accurate with Taamey Mikra
arond 90% with Nikud and without Teamim
Stylistic sets 09-10: sheva na\nach qamats rachav/qatan dagesh kal/hazaq
Stylistic sets 03-04: to fix these glyphes un paragraph styles
So theres your ansawr