Tuning Advice

The factory programming is a very good calibration, so the idea is to make as few changes as possible. I used to think the idea was to change everything too.
Now if you've done things such as a cam swap, Bigger block, forced induction, then yes - you can drastically improve the way your engine runs. 

The biggest difference you can make is in the timing tables and power enrichment tables. 
1. Power enrichment is tuned on a dyno with a wideband oxygen sensor. The purpose is to calibrate your fuel mixture at WideOpenThrottle, for both performance and safety.
2. Timing, or Spark Advance, is changed to optimize cylinder pressure. We know Torque is the force the turns the crankshaft, which turns the tranmission, the driveshaft, the differential, and finally the rear wheels. Torque is the force that builds horsepower, so what builds torque? Cylinder pressure. Cylinder pressure is dictated by cylinder filling, this is where the famous "air pump" analogy fits in. More air equals more air to mix with more fuel, which when ignited at the proper time allow for peak torque output. 

This is why timing is so important. 
Too much timing and the flame builds pressure working against the piston in it's upward stroke.
Too little timing and the cylinder passes the top of it's stroke before the combustion occurs forcing the piston downward too late.

So why I spent so much time explaining the basics? Because other than component changes, like gears, injectors, etc.. these are the two areas you can focus on that will give you the biggest return on your time invested tuning. 

Hope this helps,
-Christian