This is the first and only version I've played, so I don't know what the problem is. I did experience the "acts" progressing super fast, while I was still completing quests from previous acts.
Thanks for the save. I tried it and it seems consistent to me.
For day 49 the progress is OK. Items you had were representative for the time progress & act.
Played with your save for a while:
Cleared the Insanitarium and got the Scroll of rapture, gave Gwynn the scroll, nails and crystals, asked her to research the crystal plug, which she did and played for a while, ...
Even went to the Insanitarium again and got the spider already.
Couldn't see anything wrong with the save
Some quests are concurrent, some are independent, so they might trigger shortly after each other.
Also acts are linked to character entering the tower, so if you pushed of Nyx for a long time and then have gwynn appear a few days thereafter it might seems fast.
In short, nothing seems wrong to me with the save, perfectly fine to continue to the endgame imho.
Tested on my mac with V0.9b.1.