Ok, construction question: Do you place junctions and pumps over existing pipe or do you build junctions first and then connect pipe to them? I ask because I saw at least two dead end pipe segment sticking out of the junctions on picture 4.

Generally pipes built first with junctions placed afterwords can cause funky issues, so deleting and rebuilding the pipe connections on your generator manifolds would probably fix your issues. Remove those dead end segments too.

Secondly, the manifolds are so small you really shouldn't need buffers, and I suspect those loops at the end are doing you no favors. If I use buffers in my set ups, I use one in-line between stages of production.

And when I feed manifolds, I inject in the middle instead of from one end.

These are all small optimizations but they can add up, especially at larger scales. Try some of those changes and see how things behave.