Explain to me how you have it wired? It sounds like you connected the media bin harness to the wrong spot. Sounds like you have it in line with your cup holder? if thats the case it will kill the cup holder and the rear lights.
are you talking about the clear tube that directs the light? if so, no you cant buy that separate afaik. you can superglue it back togehter it will still transmit light just fine. If you opened the package youre kinda stuck with it. Ford is big on not taking electronic parts back once opened.
the light ring in the cup holder gets light from the lights attached to the bottom of it. if you look at pictures of the -CB youll see the 2 parts im talking about.
For the cup holder, I would order a -CB cup holder, if it comes with the lights thats even better, you can use the light holders to hold the LEDs. Check out ebay for a t5 LED light like these
White 20X T5 5630 2-SMD Wedge Car LED Dashboard Interior Light Bulb 70 73 74 18 | eBay
You can...