I'm not sure I'm understanding you correctly, but I'd be happy to help. Roofs will only attach to a full sized wall, so if I am understanding you correctly, the half wall will not meet the roof no matter what you do. Kim Emerald did a video on an easy garage door to make. You can watch it
here. Also, you can google Sims 4 noCC garage, and a lot of images will come up that might give you some ideas.
As far as the chimneys, if you are using the models in game, you can make things bigger or smaller by using brackets "" after turning on move objects. If you don't know how to use the cheat codes, again, Google is your friend. Just do a search on "Sims 4 cheat codes" or "Sims 4 move objects code." You should easily find step by step instructions on how to do it. (Honestly, I wouldn't mind just telling you, but I'm not sure off the top of my head if I'd be violating the forums rules.
This might not help you, as it makes the whole thing bigger or smaller, not just in height. I normally just build my chimneys. To do this, just build full sized walls in a square or small rectangle, however large you want it to be on every floor to the roof. On that level, I might use half walls with a trim, depending on how tall I want it, or such. You'll have to play with it a bit to see what you like.