Some very good advice from both of you. Kinda wish I knew all this from the start instead of blindly following the video tutorial link from the wiki that claims that each village has to have their centres at least 85 blocks away from each other.
I've definitely seen what you mean about the golems clogging up villages as that's happened a few times. That would be difficult to fix though as I'd have to replace the water for each cell after widening the hole.
The collection method won't be as difficult to change but will take a lot of resources and I'm assuming some sort of clock circuit to get the items transported in droppers.
Edit:
I've thought of a design that might work, but it will take a while to build:
I've tested on single player, and a 4x4 hole works fine and means I wouldn't have to change the cells much - I'd only need to extend the holes and places signs inside it. The water would create what appears to be a 2x2 hole, yet the golems can fall before they reach the middle, even if 2 clash. This would require a 4 wide stream leading into a 2 wide stream.
If I do this for all of them (including the centre) I can channel them into a killing mechanism just off the first cell but far enough away that it doesn't put them into other villages. Hopefully.