Sounds to me like you are trying to avoid something which cannot be avoided.
Cleaning up your metadata manually is your only option. You either manually set the "correct" publication date, and/or you manually correct the series column information. It can be a painful task given how much junk is in the sources that Calibre can automate from but that's just the way it is unfortunately.
The only other "up/down" thing I can think you meant was the ability to select a bunch of books to indicate they are a series (regardless of whether the series column is populated). Then with a right-click display them in a popup dialog list that you can move them up/down in, and when you click ok it writes that out as a series overwriting the numbering based on what you did in the dialog. That could be done as a GUI plugin and might be useful...