You might try gear#ead and truck source diesel. They are both known for running very clean.
The bullydog, edge, and other canned tuners can be pretty powerful... but you would never run them again if you got into the timing/fueling tables and saw how bad they are for your truck.
Custom sct tuners can usually get the truck to spool faster, run cleaner, run safer, shift better, and add custom options.
My favorite is the Super panty dropper fom TSD. It spools fast and clean... it also makes the truck feel 5000lbs lighter on the bottom end. Their tranny shifting is smooth and firm without banging around. Here is their email.
[email protected]