Tuning is VERY simple, as long as you have a fuel controller (piggyback) or a stand alone system. Whatever the case, you have control over injectors (hi or low imp) and (very desirable) timing control, also known as spark control.
In dial in safe AFR (air-fuel ratio, the amount of air and fuel entering the engine) the preferred ratio is 12.5:1. Meaning 12.5 particales of air to one partical of fuel, but that ratio is for WOT (wide open throttle), while cruising and idling situations, one should expect to dial in 14.7-15.1:1. If you get a bone stock car (toyota corolla, ferrari enzo), and you stick a wideband O2 sensor in the exhaust (before the muffles) you will see those ratios (+/- 1%).
Timing control is very tricky, factory cars differ greatly in timing control, there is no real baseline. Some cars have a total timing of 33-34 degrees BDC (bottom dead center), some have more advanced such as 27-30 degrees BDC. The only way to know i you are at least safe, is to have a knock sensor and an EGT (exhaust gauge temp) sensor. The knock sensor should be hooked up to the ECU (stand alone) and programmed to retard ignition automatically once knock is detected (milliseconds before you even hear it). EGT's are usually in the 1,500F (+/- 50F)m but it is not uncommon to have 1,800F, but that is the limit, anything more and you are asking for trouble.
High EGT's occure when you have too much retard ignition, so one would have to advance ignition untill the EGT's are safe. If knocking occures with , then one should examine the load vs RPM chart of timing, there would be a couple (or more) degrees. For turbocharged cars, the rule of thumb is for every 1psi boost increase, 2 degrees retard should be applied (total timing).
There is no way to monitor timing, all you have are results from exhaust temp and knock, unlike wiebands and AFR....... I have literally seens shops here (no names) that hook up stand alone systems for Dhs 15,000 and just dial in whatever fuel (+/- injector voltages) and timing THEY ASSUME, nothing is taken off gauges and or the dyno......
Hoep this helps clearing things up......
Here are a few modifications one could do without touching the AFR or timimg:
Exhaust system (headers/mufflers, bigger system, etc). dos NOT require tuning, since the engine is still taking in the same fuel and timing.
"Sports" are filters, i never saw even a 1hp gain from them, but still teh amount of air MEASURED by the engine is still the same, thus no tuining.
Upgraded ignition systems, no real big HP numbers, they just make up for lost power set by factory systems, no tuning needed.
Adding camshafts, ported cylinder heads, bigger valves, turbochargers(bigger, smaller or stock but faster spooling ones) DO need tuning.