As you know this is an awesome game but somethings are confusing so I'm going to share my experience (kinda basic but I hope it can help you. I'm playing the previous version (1.0.1) and this is what I found:
Pinktea made the biggest troll in game by adding an event that ruins the story it requires you playing with Clare in the kitchen using the backdoor and putting a cucumber in the front door will move your affection value to 5-12 and discipline to 27 saving the changes in that moment, don't go to the kitchen if you want to see an ending different to PUNISHMENT.
The game endings depends of the values of discipline and affection, with both under 100 Clare becomes a Dispirited girl, 400 of discipline and negative numbers in affection makes her Timid both "ranks" gives you the PUNISHMENT ending.
**Update. Thanks to damianea103 it seems that you can get Timid with at least the double of discipline.
With 238 of affection AND discipline Clare becomes Keen and it unlocks the HAPPINESS ending. In order to don't lose points of the values you must reward her for successful tasks and punish her for fails, also the rank upgrade events gives you score for it so about tasks in the first ranks try to pass without chose the third training answer (up to down) for her fails and use the hard task difficulty when it has a chance of 50% to be clear in the rewards and punishment if you requires to increase her affection or discipline but her result for a task is incompatible just go to main menu to repeat the day until she do as you need (reset the day is a life savior except for kitchen event).
Talking about the rank upgrade events it doesn't require a deep explain, just do as you need be rude for discipline and sweet for affection, Clare is intense and you can call her a freak or whatever that makes sense to get affection or discipline, and since when you get 100/100 experience for each rank your training doesn't gives you more score wait to that point to tal with Clare about past and anything, those chats increase your score (depending of your answers) beyond the training limit and each rank has its options.
I don't know the use for the values of the "backdoor", "oral" and "arousal" but my theory is that ranking the max of them unlocks a secret event but is a theory hard to verify the backdoor can be upgrade 6 points per day (2 battles in the "play" menu, chose bedroom and follow it to finish in her backdoor *only after rank 3 or 4 and is limited by rank until Clare gets a final rank "Keen, Dispirited etc.") it seems that fail o succeed in a task is irrelevant for to upgrade this value. Oral can be increased 9 ponts per day (in the reward section chose "watch TV,, then hand in her leg and the next is obvious) if you try to upgrade her backdoor first the oral event disappear that day and you have to wait for the next.
The Arousal value increases with both punishment and rewards, in punishment you can continue even after the end option displays to give Clare an orgasm by spanking or absolutely whatever punishment you chose to do I mean all that you want to do just try to put her eyes in the sky, rewards are kinda boring but with exception of only "watch tv" all works, and "s. battles" where it works as long as you don't finish in her, so you can play rewards or punishments just to increase this value up to 100.
Right now I'm in day 80 in my HAPPINESS save, affection is in 276, discipline 238 and those values can't go further (it can go down by the kitchen) the backdoor value in in 303, oral in 114 and I think that I will forget about try to reach the max scores since 6 ponts per day means 50 days to get 300 points and if there is a true limit for the backdoor and oral is unclear.
I don't know what came with version 1.0.2 , I read somewhere that it has new costumes and 2 new finals but if I install it and it deletes my progress it will be as the cucumber, anyway I hope this helps you and if you know something about this game or you have information from version 1.0.2 please share it.