Use the machine in the center of the room you found Kari in.
I'll have to do some testing but if you can only make the base then I think you didn't find the parasite removal terminal entry in the main lab terminal. Unfortunately you can't reach that terminal if covered by the squidrabbit. Something in the Manor should be able help you. If I had to guess I'd say to try getting possessed and walking in front of a mirror. You could then try to enter the lab from the manor and see if the scanner door will let you pass. You might need to do that twice and take the secret path to the other bathroom. If you read how to remove the parasites you should be to craft the C-ALPHA. Three of the needed vials are located in various rooms. You need to mix the Protein Base with the purple vial and the other item to get the last required vial. You should then be able to craft the C-ALPHA. Otherwise you might consider starting a new save file where you explore the lab more thoroughly before encountering the squidrabbit.
EDIT: If you get possessed and can open Lady Jessica's Door, then you interact with the door while possessed so that it will let you enter. Enter AFTER the possession expires and look in the mirror. You will have enough time left to get to the lab and to the terminal with the information for the parasite removal. You should then be able to craft C-ALPHA and C-DELTA. The other recipes for the Protein Base need to be found in terminals or after using a specific item located past the squidrabbit.