Hi! To align the choice buttons to the left, set the xalign of the choice vbox to 0.0 (you can find it in the style section in the choice_screen.rpy). To make it smaller you can change the text size of the texbutton of the choices and edit the graphics to be smaller (might need to adjust the frame borders too) or you can create a transform which sets the "zoom" to a number smaller than zero:
transform small_choice: zoom 0.8
Then add it to the textbutton:
textbutton i.caption action i.action at choice_delay(t = idx), small_choice
As for the out of place buttons please specify what you mean and how you implemented it. My guess is that there are some stray styles leftover from a default project or a file wasn't copied but I cannot see your game or code.