First of all, mad dedication bro. I would not have that kind of perseverance for a single achievement.
Anyways, I managed to get all the achievements recently and had this problem with a few of them. Restarting the game and keeping track of my catches worked eventually for "Get Over Here", but if all else fails you could try making a backup of your current save, deleting the game, and then redownloading with your loaded backup (the save is in AppData > LocalLow > HotPink and Annue > Tentacle Locker 2. Grab the TL2 folder and save it somewhere that isn't in AppData, then put it back after you redownload).