Open up the Cloud_Fix_EA.event file, scroll down to line 49 or thereabouts, and replace the stuff after Cloudy_Sprite_Attributes:
with the following:
SHORT 27 //number of objects
//Row 1
_64x32(0x00, 0x00, 0, 0, 0)
_64x32(0x40, 0x00, 0, 0, 0)
_64x32(0x80, 0x00, 0, 0, 0)
_64x32(0xC0, 0x00, 0, 0, 0)
//Row 2
_16x32(0x00, 0x20, 0, 0, 6)
_64x32(0x10, 0x20, 0, 0, 0)
_64x32(0x50, 0x20, 0, 0, 0)
_64x32(0x90, 0x20, 0, 0, 0)
_32x32(0xD0, 0x20, 0, 0, 0)
//Row 3
_32x32(0x00, 0x40, 0, 0, 4)
_64x32(0x20, 0x40, 0, 0, 0)
_64x32(0x60, 0x40, 0, 0, 0)
_64x32(0xA0, 0x40, 0, 0, 0)
_16x32(0xE0, 0x40, 0, 0, 0)
//Row 4
_64x32(0x1F0, 0x60, 0, 0, 0)
_64x32(0x30, 0x60, 0, 0, 0)
_64x32(0x70, 0x60, 0, 0, 0)
_64x32(0xB0, 0x60, 0, 0, 0)
//Row 5
_64x32(0x00, 0x80, 0, 0, 0)
_64x32(0x40, 0x80, 0, 0, 0)
_64x32(0x80, 0x80, 0, 0, 0)
_64x32(0xC0, 0x80, 0, 0, 0)
//Row 6
_16x32(0x00, 0xA0, 0, 0, 6)
_64x32(0x10, 0xA0, 0, 0, 0)
_64x32(0x50, 0xA0, 0, 0, 0)
_64x32(0x90, 0xA0, 0, 0, 0)
_32x32(0xD0, 0xA0, 0, 0, 0)
Now, depending on how large your map is (and this goes for the version with the hole in it as well), there may not be enough sprites to cover the whole thing on the bottom. This is because for every square (16 pixels) you scroll downwards, the sprites move 3 pixels. Thus, you have this result:

in which case you’d need to add more sprites to the list above. Just ask me if that becomes necessary (or, with a bit of pattern matching, you might be able to figure it out yourself).