I used to have on '08. I now have a '99.
First thing is always, tint.. Blacked out.
Level kit with some decent meaty tires. I added a new head unit and subs soon to follow.
I wouldn't do any bra unless you do that clear paint one like you mentioned. Tool box and bed liner yes!
Mine now has a camper.. So I do not need both.
Loved this site,
http://www.fordf150.net/ for when I had mine.