sunilp,
Congratulations on the new truck. You will love the power and ride.
As for fuel economy, I wouldn't touch it for a while. I know my 6.0 just kept getting better and now my 6.4 seems to be doing the same. I have almost 14k miles now and I'm going to put my programmer on tomorrow night. I was going to do it sooner, but I wanted to wait til the motor had a few miles at least.
Your question on 3.55s...I highly doubt any dealer will change them under warranty. It would be you paying for parts/labor I'm sure. Personally, I wouldn't spend the 12-1800 on having them changed out. For that much coin, I'd do a Spartan Diesel Technologies programmer/dpf delete and get twice the mileage.