After replacing the scripts.rpa file, the game gives an error and crashes.
If it's errors like :
The label _call_pause_scene_703 is defined twice, at
File "chars/char_Mary.rpyc", line 1386 and
File "chars/char_Mary.rpyc", line 1499.
you need to download the last version of the mod, released yesterday.
if it's another error and/or you already use the last version of the mod (1.06) then what is this error ?
I also couldn't load older saves so I had to start a new game.
Which is the reason why you don't see some parts of the mod.
In order to stay as near as possible to the game spirit, I put some conditions related to Billy capacities. By example, it would feel wrong to be able to suppress "Family ties" for the mother, before Billy have the mind control power. It also have a practical use, since it ensure that the player will not make possible game breaking moves.
As for the "Perks, Flaws and Improvements" part, it's disabled by default. Initially it was because it's a too cheaty part, but now that there's the scenes tracker, I'll probably change this ; this part being now mandatory in order to see all the scenes.
This said, what prevented you to load those saves ?
Is it because you get an error saying "AttributeError: 'NoneType' object has no attribute 'sensitive'" ?
If yes, I answered this
here. It's an issue that happen time to time when you pass from a compressed version to the original one, or the opposite.