Hi Misterxus.
Yep, we all are in the same boat. As new versions show up I will remove fiche versions when paper appears but we decided to keep alternate paper versions on the site and allow each member to choose which they decide to keep for their own collections.
Personally I just unzip into a folder, rename as needed, and then rezip the file. Rename to cbz and file it with other issues of the same title.
I haven't tried GonVisor or either of your zip programs. For fast edits to crop or straighten pages I use Irfanview but remember, when working with a jpg each resave will degrade the image. So I do all my changes, sharpen once and save at 85% which usually results in a larger file than the original.
-Yoc