Right, apologies for the lengthy delay, @BetweenWalls. Took a while to figure out how to get the pipe graph built, with life being hectic. I haven't implemented the upgrade sequence yet -- I'm still debating the best way to do that in terms of where to put the functionality (w.r.t. user controls -- a separate tool, on top of the belt tools, etc.). But the graph is built and that's very easy to reuse once I figure out where I want to put the user control for the upgrades.
@TeabagNation, the removal of pipelines has been added to the existing remove tool in version 1.4.0, you will have to use the reverse_selection option (by default, right-click and drag). This should remove all pipelike entities (pipes, pumps, storage tanks, etc.), but no crafting buildings. Lemme know if you find errors.