Hi, the black streaks that you mention, do you mean the dirt spots on the top of your bumper on the picture? If yes, that's normal. The rear of a CT gets dirty very fast when driving in the rain. It's just caused by the design of this car. Some people fitted mudflaps and it supposed to get less dirty but I can't tell for sure since I haven't fitted those.
The part that's missing is this I think:
Cushion - Lexus (75129-AC010)
parts.longolexus.com
Good luck!
The part that's missing is this I think:
Cushion - Lexus (75129-AC010)
2002-2018 Lexus Cushion 75129-AC010 | Longo Lexus
2002-2018 Lexus Cushion 75129-AC010
Good luck!