Hiya,
Since you are building a new intake tract, use the 01-06 Truck MAF, it is much more forgiving to intake tube changes(Initial tune I posted is set up for that). Make sure it has at least 12" of straight tube after the MAF, and a high quality air filter before the MAF that will reduce any turbulence before the MAF. These things will drastically help you in the tuning process.