I just did this. Unless you are fluent with doing this job, you will never finish before the ecu is returned back to you. I sent mine out on monday am and had it back wednesday am. It was perfect timing. I do believe you need to have Roush do this to get the warranty. At return of the ecu there is now a new sticker on it that says "call Roush before programming" or something to that effect.
Fwiw, my car lit right up and seems to run just fine with no other electronic modifications or adjustments beyond what came with the standard package.
However, at this point I cant tell if I left anything on the table or not. Going to have to find a dyno somewhere to find out. Expectedly this car should now produce 380 plus rwhp. If not...somethings up. Seems to run fine but I feel (or percieve to feel) a slight missfire somewhere in the low rpm range. This is only a perception so take that statement with a grain of salt. It could very well be right-on for all I know.
Personally I would do it the Roush way by-the-book at least in the short term and take it from there.