What custom functions do you need to access? No, nothing can be changed from the camera, but there's always the 550EX's custom function menu. Hold down the backlight button for 3s or so, and you'll be in the custom function menu.
As for the functions themselves, you'll need the manual or some reference to tell you what is what, because you're only going to see CF 4 01, telling you that custom function 4 is set to value 1.
There's no nice description of the settings there, but you might not even need to play with those at all.
You still have a powerful shoe-mount flash that's able to control others via Wireless TTL, and can be a slave itself. It's a steal at under $200 (Just bought two of the BGN quality ones myself, after downgrading from 580EXs), and they're still much more feature-laden than anything that YongNuo has come out with yet.
External speedlite control only came with the 40D/1D Mark III, and this flash is MUCH older than those units, so isn't compatible with those camera-driven controls.
It's a completely normal 550EX, and is functioning exactly to specifications. There's nothing wrong with it.