The DF map site is Dwarf Fortress Map Archive or DFMA in short.
http://mkv25.net/dfma/From the sound and looks of it, your well cistern is WAY too BIG for the water source you are drawing it from.
I always pave the inside floor of the well with stone block floors to prevent muddying as well as to prevent unsightly moss and tree growth, something I learned from making multiple waterworks for my forts that don't choke over time. You'll want to pave stone floors over everything that the water comes into contact with though, including the interior of the pipelines and the floor that supports the pumps. Your game, your call.
If you want to retain your mega well, increase water intake. More pipelines from the east. I think 3 more will be barely enough to cover the right side in water, but... you'll need to pump continuously i think. But really I doubt it will work. I make underground pastures 31x31 and it takes years even with continuous pumping for the water to reach from one end to the other, much less fill it to the brim.
BUT REALLY YOUR CISTERNS ARE BIGGER THAN MY GRAZING PASTURES. I would suggest 2 separate well cisterns 5x5 and 2 z-levels deep or no bigger than 12x12 and 2 z-levels deep. Wall up if you have to.
I understand that us dwarf overseers like to make excessively huge megaprojects, but this is just impractical.