I wouldn't go deleting playlists indiscriminately. This is likely to give you a menu that is mostly broken.
You should probably try BD Rebuilder if you want some menu options. There are several modes in BD Rebuilder that give you menus.
The Full backup will be a straight copy, if you set your output to a BD-50. I'm afraid this might not solve the jumbled playback however, as I'm not so sure your disc was decrypted properly. You can try this however, as it shouldn't take much time. Now would be a good time for a 50gb BD-RE disc to test output. I don't know that you'll want to waste a 50gb BD-R disc if this doesn't work.
You can also have a Movie and Menu with the extras automatically blanked out. To do this you would have to enable Blanking and Edit mode in the INI file. Read my guide for BD Rebuilder using the link below, in my signature. You could, with this type of backup, chose which extras to keep by right clicking on each to Preview them. To get them back into the movie and remove the red X next to the ones you want to keep, double left click on them.
And another option is the Quick Start mode. In this one, a new, simple menu is made, so I doubt you'd want this. This one jumps straight into the main movie, but you can access the extras through the controls of your player. When making this type of backup, you also get options on which extras to keep. Since BD Rebuilder automatically chooses only those items of a certain length in time, you may lose things like previews of other movies. The length of time can be adjusted, so that more items are included if you wish.
Some of this is a bit complicated, but reading through the guide should help.