I can't answer all your questions definitively, but I can answer the change the menu one. Click on the restaurant and go into build mode.
You will see the box in the upper left corner of the screen where it says the lot type. You at the top of that box will see what looks like gears. Click on that. You will see the option to customize menu. Click on the box with a fork and a knife. It will bring up the menu and then you click on the box with a plus sign in each category to change the options. You will have to unclick those options already chosen you don't want if it is an ea built restaurant. Then just choose those options you want. Remember there is a limit on how many items total you can have throughout the four categories.
The only way I believe you can have some control over staff is to own your own and hire the staff yourself, but I think you have limited options as there is a list of choices to choose from, but not sure 100 percent on that as I have never owned a restaurant.
I sent my sim to the library in Oasis Springs and there were skill books there, so maybe you have a glitch or a mod conflict perhaps?
If you have mcc you can change situational outfits and have it default to the category option of your choice. If you don't have mcc I don't think you can.
I hope the few I have answered helped. I hope someone else can answer the rest and if I got something wrong correct me.
