Extracting: Hipster. Instructions on the page.
Editing: Photoshop.
Repacking: ????. No one has made a repacker that I'm aware of.
Are you talking about the PC version of Calamity Trigger? I can't guarantee that Hipster will work with those PAC files. But you can try it! If it doesn't work, then you're boned, unless you know how to work with QuickBMS or something like it, which should also allow you to repack them later.
Also bear in mind that stages are 3D, so unless you're going to rip the stages and replace their models with flat planes, you're gonna have a hard time making proper 2D backgrounds. Actually the entire game is 3D, the character models are just flat planes with sprites applied.