I had lot's of issues with this fixed version as well, until I made a clean re-install and started all over without Incest Patch. Have to say I don't know if the patch causes problems or not, but just to be on the safe side I didn't use it.
Now to explain how I understand the problems to occur:
It's related to the old saves, even if you delete the game and install the new version and start a fresh game, you still have a hidden save folder which links to the game, messing everything up.
This hidden save folder is located on another part of your hard disk. If using windows it's in your AppData.
How to locate it, for Windows 10 at least:
C:\Users\"YourComputerName"\AppData\Roaming\RenPy
Inside this hidden RenPy folder you will find save game folders for all your RenPy games, locate the one(s) for:
My_cute_roommate & My_cute_cousin (if having played the game before the change)
Delete these folders before or after you delete the game folder.
Now everything related to the game should be cleaned from your computer.
Install the newest game version.
Start a new game and now the game has created the RenPy save folder inside your AppData once again.
Everything should be fine and you can enjoy the new Game Version without any bugs.
If you follow the story as it's mend, read the game hints as they appear, only use the Walk Through if truly stuck (which you shouldn't following the in game hints) you will be able to reach all contents and get all Achievement Pictures, except for one which I should have gotten but somehow it didn't appear in the Pictures. Was the one for First Photo shoot of Roommate/Cousin.
Also want to inform on the Trainers Boob picture:
To get this you have to have read the second massage book, Intimate Massage.
Ask to massage the Trainer again, do NOT use the special massage Oil, Massage her back, shoulders, back and click where your finger is pointing at her back. Do not try to massage her ass or legs.
She should at this point turn around exposing her breasts and you have option to massage front part. To get the picture go for the breasts, she will get mad, but that's how to get the picture.
Make a back up save before asking to massage her, just to be sure to be able to backtrack if something goes wrong or my instructions wasn't 100% accurate. (I did this a few days ago so the exact massage point order may be slightly different.)
As stated above, I manage to get all scenes without any bugs. I did use the in game cheats without getting bugs. Took a lot of hours to play it all again.
Advice to get the First shower picture as soon as you get the screw driver, before the Roommate has Hearts.
Advice not to masturbate at any time in the shower as this will create broken heart for Roommate, regardless if cleaning up the cum or not (might be a game bug not yet fixed, but not a game breaking one.)
Use the cheats to increase Potency, or increase it by all the other in game events, such as the Nurse blow job etc.
I did masturbate in the shower one time, at the game beginning, to get the conversation question from the Roommate on what the noise was in the bathroom, you know at the first kitchen conversation.
This did create one broken heart, so in my game end I had two hearts, where I might have ended with 3.. I don't know if 3 is a possible ending score with her, but was curious that another girl had 3 so suspected the 1 shower masturbation could be the reason for only 2 in the end.
Last advice: Make a lot of saves, before any new event, just to be sure to be able to backtrack if you played anything in a "wrong way or order".
That's my rambling for this time, hope it helps those who still has issues/problems with this game, cheers