The maximum length or width you can have for any object in EggVine is 80. Whenever you make an object bigger than that, there's a high possibility of it glitching up as you've described. This seems to be the case for you, as you said your water stretched across the whole level.
This can easily be solved by just duplicating any objects after you reach the 80-tile limit. ;)
As for your vanishing sprites, that sounds like you have a lot of sprites in one area. Are they crammed in one concentrated area, or did you spread them out across several screens? In YI hacking, sprites will tend to vanish if you place too many, rather than causing slowdown like in SMW. My advice would be to just move your sprites around to different spots until they load properly. Also, the door sprites take up a little more sprite memory, so try not to jam too many of those into really busy areas.
This can easily be solved by just duplicating any objects after you reach the 80-tile limit. ;)
As for your vanishing sprites, that sounds like you have a lot of sprites in one area. Are they crammed in one concentrated area, or did you spread them out across several screens? In YI hacking, sprites will tend to vanish if you place too many, rather than causing slowdown like in SMW. My advice would be to just move your sprites around to different spots until they load properly. Also, the door sprites take up a little more sprite memory, so try not to jam too many of those into really busy areas.