Always do bodywork last,because it always has to be paintmatched,and in the time you install the kit,you might to oter stuff that might need painting too,plus,you pay for the cost of the kit,and then you pay for installation and then you pay for paint....yeah,it adds up fast.
Go for wheels. Don't get anything stupid though. I went from the stock 14" steelies on my car to 16" Contour SVT E1 rims. My car is not lowered yet,and it looks fine. It sits like a stck SVT. I'd say 16's are about as big as you need to go if you're not planning on lowering the car anytime soon. If you get 17+,they'll be big,and with low profile tires,you'll look like a 4x4. The Focus wheels are definetly hot,imo,go for them if you can get a hold of some.
But yeah,do your bodywork last. I molded the tail lights & plate frame on my trunk,and needed to repaint my trunk,but my car is getting repainted in the spring,so I wasn't going to spend $250 and have my trunk painted to match again,so I just rattle canned it flat black for the time being. Looks uber ghetto. Perfect lesson of why not to do bodywork when you're not gonna paint the car right after,because your car looks like a stupid riced up car with an owner who can't afford to paint it.
Wheels are always classy. Add wheels to a stock car and it totally changes the look of the car.