Add a new feature to the extraction module (or an advanced one) that allows for more options. One option could be a "per redstone signal" extraction feature, allowing the module to extract one stack per signal. Another one could be an option allowing you to set how big stacks should be.

EDIT: will be adding comments with suggestions.

Extraction modules seem to have the per-pulse feature by now.
The balance module you speak of can be achieved by using stock modules, which is also more intuitive than color coding chests and having it compare their contents.

How about this:
A balance module. It is color coded, you can color it in a similar way to how you color ender chests. 3 colors. In your Relocator System you add these to relocators connecting to inventories, and inside its GUI you can set what items to keep balanced. So, if I have a red-red-red one connected to chest one, and a red-red-red one connected to chest 8, and I put stone in the GUI, it will automatically make sure that there is as much stone in chest 8 as there is in chest 1.
I also have a red-red-black one connected to chest 8 and a furnace, keeping the coal balanced between these inventories.

I know that there currently is no "grid" in the Relocator System, but I think this would be a nice thing to work on, and I think it would be useful in many scenarios.