I Have a stock 08 6.7 2500 the only after market addon is a banks cold air intake. I bought a Hypertech Max Energy programmer and installed the stage 2 program. The truck has noticably more power and I now get 3 more mpg.
only thing is, the engine sounds louder, it seems to clatter when I first start it then goes away, but when towing you hear engine drone in the cab. is this ok ?

 

Changing the tuning to an engine changes the way it runs and sounds. I would say it is normal.

Id just keep an eye on things as the Hypertech may turn out to be less than DPF friendly.

 

Timing is the clatter you hear. Have to be careful with the programmer you choose, too much timing may cause some other issues. But get some gauges and keep tabs on it, sounds like the hypertech jumpered out the EGR for you at a minimum.