When cleaning up with the wrench each node (item, fluid, energy) has its own ID and doesn't stack in my inventory, as it is a unique item. Can you make it so shift left clicking pops the item off and drops the ID just like if you painstakingly mined it?

I think this would be very confusing and accident-prone. If you accidentally click it would delete all that precious data unintentionally. I think it would be better if it requires a different type of item, or a selectable mode for the wrench item. Some warnings or safety is needed to help discourage you from accidentally deleting data (similar to why mining a cable/part takes a long time).

The connectors should craft into their brand new form.

I guess that my particular use case is too niche. I was using the pipes from this mod to handle my main bus and when doing cleanup of an area I was finding it annoying that my inventory got filled with these connectors rather than, like most mods, collapsing into a single inventory slot. I guess the pipes do collapse but the connectors, something that the rest of the piping items in other mods just automatically create, are a separate item that just adds overhead to using this mod. Needing to craft them, manage them, detach them, recraft them back into vanilla connectors, felt like a severe negative thus balancing out the amazing usefulness of the rest of the mod, so the tedium made the mod balanced. It seems that having connectors with specific IDs and retain them when dropped provides enough value with no easy way to retain that feature while also being intuitive and fool-proof. It makes sense now. Carry on.