Alright, I've looked at your save.
You are not being affected by the Questline_main or misc quests disappearing.
The journal indicates that you should advance your massage skill, but the online course says that you're done.
Taking a look at your variables you have edited them to impossibly high values
MassageCourse_Level is at 100 but maxes at 11
QuestLine_Sister is at 101 but maxes at 6
Questline_Aunt is at 10 but maxes at 6
Questline_main is at 10 but maxes at 9
Questline_Mother is at 2 but maxes at 10
Edit: Questline_Misc is at 10 but maxes at 3
You are also missing variables that you should have
It seems that you have broken your save through editing the values. This has caused certain triggers to not fire off as they should and simply be skipped causing you to loose access to scenes in this version. This will also potentially cause you to skip scenes in the next version.
Edit:
SSG_REY
Edit:
I'd recomend starting a new save to make sure that you've seen all the scenes available and not editing the questline variables. Use the journal to figure out how to progress each character. Use console commands to make sure everyones lust is as high as you want (anything over i think 30 should do the trick, but don't quote me on that). With that and being careful you should be able to see every scene in 30 game days or less I think due to the requirements for getting the dreams and visits from Enlil.