Some iconic weapons/clothing can be upgraded to higher Tier. You do it through the crafting menu, so you need points in Tech and the necessary Perks. Then you simply craft the item from the list.
Yeah you can't upgrade rarity. You can craft some of the items to a higher level, but the old one isn't guarenteed to be destroyed in the process, leaving you with extra weight.
You can't, but you can download mods that will allow it. At this point in the game though, with your wardrobe, it's really not necessary. Just wear the legendaries you find and use your wardrobe to determine how you look.
