Some less expensive kits require the builder to improvise. If you run into something you can't figure out, post it here and get help. Some kits require you to drill holes in the chassis to mount things. It may not be what you expected when you purchased the kit, but do the best you can. These kits require some tools and experience so they are not for everybody.
1) I can only guess but prehaps they are to provide a place to solder unused wires from the transformers. Check the wires coming out of the transformers against the layout. Any extra or missing wires?
2) Wait until the cabinet shows up. They may be to mount the baffle, speaker or chassis.
3) I think you are correct that it is the extention speaker jack.
Did you know there are people who sell kits for automobiles? Imagine trying to fit a sports car body on an old Volkswagen chassis.