In the saved games of the raw version that you downloaded, there should be a 100% clear save in the first slot that has the main storyline completed. Load that up, go through all the "reward" h-scenes that are unlocked after completing the guild's quests for each area by using the bed in the MC's house and choosing to sleep with Sana. In the fourth and last of these scenes, Sana mentions that she's no longer taking the pill. Once pregnant, Milk will show up and talk about how she owns a house outside of town and that she'll watch over the kids. Go there, and there should now be three kids running around with all of the content there being be accessible.
Note: If, in the 100% cleared save that comes with the raw, Milk's house is already unlocked without you having to do anything, then you'll run into the problem with the children not showing up as you did before. An indicator to tell if your cleared save is the right one or not is if upon loading it up, if it starts in the memory room with Sana following you. If you start there, then you've got the right one.
Also, if by "the baby scene" you actually meant the scene where the doctor has sex with Sana while she's pregnant, then you can get that by waiting at the entrance of the clinic once Sana disappears after you get the pop-up message stating that she's pregnant. There should be one of those sparkling lights outside her room indicating that there's an h-scene there. The doctor will also be in the room. If there isn't, pass time until a full day passes whilst outside of the clinic until they appear. If the light still doesn't trigger after passing time for a whole day, then that may mean the MC was asleep whilst this scene was happening. In this case, you'll have to experiment with getting the "Sana got pregnant" pop-up at different times of the day until you're awake when the clinic scene is happening.