The Little Hole is the Output, note the Side where this black Line is too. You set them up right
I am currently looking your Stream but it seems you didn't saw my Comment
The Filter in the Nether needs an Empty Bucket, so it Only take the Empty out en fill it.
The Filter in the Overworld of course needs a Full one, so it Only take them out and empty it.
And so on until your Nether is Empty
But so this all works, the side were your an not in (Nether or Overworld) needs to be loaded. Minecraft did not do this for you and you have to force it with an Chunkloader. You have some Options for this, you using a Railcraft "World Anchor", the downside on this one is that it needs Enderpearls. One stack Enderpearls let it run for 4 Day. Put a Hopper on Top and it last for 20 Days. And it loads the Chunk where is in and 1 in each direction. (3x3)
And you can use a "Chunkloader" This one is awesome, it runs without fuel an you can adjust with Chunks you want to be loaded.
(I am using 3 Chunkloader to load my entire Overworld Base. one Big 5x5, one 1x3 only for my Wheat farm and one 3x3 for my Bee HQ)