congratulations for the time you spent doing all these screenshots and saves, you should really learn to compile so that you could try these alignment issues yourself, because you never see the end of it !
Clearly all this comes from the resolution change in this game. Now the screens to be able to check relative alignment of layers are very rare, even more so when you talk about vertical alignment ! Yeah I missed scroll1, maybe I didn't want to see it at the time, the text layer for the 1st screens, the horizontal alignment is easy, but there might be some vertical alignment too about this and in this case it might affect other layers too...
The sodom stage is the worst, this stage is done by pieces of layers stuck together everywhere !
Anyway not sure at all we'll see the end of it before long... You fix 1 screen and then you notice that it breaks another one ! Too bad there's no screen to check these alignment in the test mode, there is one but it's done only to align the crt monitor screen image, I guess it didn't make much sense to align layers on the original hardware back then... !