and we know who put the Donkey Wheel there now.
No we don't.
The MIB never got a chance to build his Donkey Wheel contraption. His mom knocked him out and caved in the well and killed all of the remaining villagers before the donkey wheel could be built.
Someone else had to come along after and re-dig the well and build the contraption.
Maybe the MIB helped them do this, but we don't know for sure that he did and we don't know who it was that did the actual work.
What is also weird is that later on we see that the MIB hated jacob for bringing people to the Island, yet from this episode it appears that it should be jacob (like his mom) who would want to keep people away from the island to protect it since they are all "evil". And it would be the MIB who would want people to come to the island to help him (and re-dig the well, etc...).
I wonder what happened over the years that would make Jacob want to bring people to the Island and what would make the MIB want to keep them away. Especially since it appears that the MIB needed people to get his "loophole" while all the people coming to the Island ever did was to get Jacob killed. If Jacob never brought anyone to the Island then he might have lived forever. And kept the MIB prisoner forever.
That's a big question/flaw in what we have seen so far that really should be answered. Otherwise the two big powers that have been pulling all of the Losties strings for so long have plans/goals/ideas that make no sense.
Perhaps the MIB came back, after becoming smokey, and finished building the Donkey Wheel. He certainly had plenty of time to do it.
I don't think Jacob ever agreed with his mom about the people being evil. He didnt' want to leave the island, but I don't think he exaxctly agreed with his mom either.