There is only one feature missing from AUP that keeps me using Advanced Fluid Handling: I can't use Flow Configuration to set flow direction(s) for underground pipes connected to the underground connector. (The GUI pops up, but there is no way to toggle flow direction(s).) With AFH, I can have 1 regular underground connection *AND 1 connection at a right angle to the underground connector within a single cell. (When I am trying to pack as many pipe connections as possible into a T1 Factorissimo building, that flexibility is key.)
It struck me that one simple change to your mod would allow the same flexibility: instead of an underground consisting of an overground input and underground output opposite the input, what if it had neither? What if it was simply a virtual vertical connection between regular underground and overground pipes that would use up/return 1 regular pipe each time it was toggled — with <CTRL-G>, perhaps?
Players wouldn't have to keep underground pipe connectors in their inventory anymore, and could connect their pipes however they want. For example, if they want to connect two perpendicular pipes — one on each layer — they could tap the 'connect_layers' key, and it would just work. (Perhaps have a mostly-transparent vertical pipe top overlaid on the connection to remind players where they are?)
Does that sound doable?