Not sure what I'm doing wrong, just mocking everything up to see how it fits. (I know it's dirty, go easy on me)
Seems like the running board needs to be raised up a bit

 

I'm going to guess that's not the original bed. I had the same problem when I bought a bed from a 57 and newer truck. Ford moved the fender mounting bolts up on the newer beds.

Other folks have had the same problem: running-board-help

 

Actually, the fender edges/bottoms hang a little BELOW the running boards...at least they did on my 48. May be different on the 53-56.

 

Exactly what Fat Fendered Ford said.

 

Hi Kevin! Long time, no post! How have you been?

 

Could I just get a fender patch and add it on to the current fender so it will meet the running board?
Mid Fifty F-100 Parts - Fender Patch Panel, Rear, Left 6" At Run Board
Also, why does my running board tilt from front to back?

 

It shouldn't. The front and rear running board supports should hold the board at the same level. If they don't, I'm guessing something is bent, installed wrong, or the rear support is from a larger truck.

Here is the normal installation. (not my truck)