Steps 1-2 are completed? Good, lets get started.
Step 3)
The most difficult time for any engine is idle. An engine LOVES WOT. I seriously spend 1/4 the time on WOT power compared to the rest of tuning (especially with my dyno). A rule of thumb is if you can't get the car to free rev in the parking lot, it is not ready for dyno time. If it can not sustain a stoichiometric a/f ratio around 2000rpm, you are not ready for dyno time. Now since this is MAS based systems specific to 3000gt ecu's, most of you should run okay and wouldn't worry about this portion of it.
A few key points to remember.
1) Fuel is used for THERMO MANAGEMENT. Stoichiometric a/f ratio for gasoline is 14.65:1. That is the chemical formula (okay I lied, tuning is mostly math, some physics, and some chemistry...sue me) for a perfect ratio with nothing left over for fuel and air molecules. [(14.68)air+C8H18=CO2+H20 +NOx]
2 Ideal power A/F ratio is 12.6:1-13.2:1. This is when you have the most power for the least amount of fuel consumption. Unfortunately since we use fuel as a means of thermal management we need to error richer than this for 92 octane. This is since our intake air temperatures are most likely higher than ambient air temperatures at the air filter AND since our fuel isn't very consistent compared to higher blends of octane (aka more prone to pinging due to lower octane).
Most vehicles I setup like this:
14.7 for
idle,
cruising, and most transient rpm throttle points.
13.5-13.0 (rpm dependent)
around 0" of vacuum or 0psi as this is roughly the best a/f ratio for peak power with the least amount of fuel consumption (remember kiddies the name of the game is responsible tuning, lets not deplete all of our available fossil fuels in 1 pass down the drag strip, let alone foul our plugs and wash out our cylinder bores) Also remember the name of the game is smooth. Make it taper in smoothly, vehicles do not like air/fuel ratios that behave like a "switch" (14.7 BAM 11.2, not a good idea).
Most sidemount intercooler vehicles running substantial boost on pump gasoline (14psi-20psi) I error towards the side of safety and target between 10.7-11.3 a/f ratio under peak load/power. I let the car tell me what it likes, but 99.992% of the time end up in that range. Remember the fact that most OEM's shoot for 3% accuracy using narrowband oxygen sensor inputs, so don't kill yourself on this one.
Cars that have better intercooling I tend to run a bit leaner as I don't need as much (drum roll please) thermal management. Most FMIC cars are 11.0-11.6 a/f ratio on pump gasoline. Again, you use fuel for thermal management. A few decimal points will help starve off the knock threshold, especially if you are higher than stock timing.
3) Timing:
Please for the love of god, log your car. I don't need a logger on most 3000gt's anymore with piggybacks, but we have done more 3000gt's to count and my dyno logs torque actively

. I know there is an factory timing value chart posted somewhere here on 3si or out there on wikipedia land, so I won't reference that, but you should be close to that.
Idle timing:
Usually 10-18, use only as much timing as you need. Idle is all about torque management You want enough timing to have have the car maintain a steady idle with minimal IAC motor input.
Most of you piggyback guys won't have much control over this (unless you globally scale your injectors incorrectly).
Cruise timing:
Most vehicles cruise with around 25-35degrees advance. As load goes up, generally timing decreases, as rpm goes up, generally timing increases.
Power timing:
Timing should ramp up with rpm except under most setups it is perfectly normal to have it dip under torque peak. As your engine reaches peak VE you will need less timing advance to obtain the same torque values. Timing is used to well "time" when you want that spark event to happen. Timing is dependant upon cylinder air temperatures, cylinder bore size, combustion chamber shape, octane, and rpm...that's it. Most 3000gt's tend to stay in double digits under peak power/higher boost on pump gasoline (less than 20psi). I would say 10-15 degees is safe. I know the factory map adds a bit of timing up top as the 9b turbochargers fall off boost at high rpm. To compensate with this lack of airflow, the factory increases cylinder pressure by timing. Most td04 cars follow the same trends (boost fad slightly), but I would highly recommend to keep your timing under 20 (actual).
Now remember they are just numbers that are being interpreted by a logger. AEM numbers and pocket logger "timing" values are not really interchangeable as each reads timing and calculates timing values differently.
*Now on race gasoline (especially 119 VP Fuels C-16) you can hit MBT LONG before detonating/knocking. This is a safe fuel to tune on, but requires a completely different gamplan. Target air/fuel ratios are leaner (read: more stable and more octane), and timing needed to keep it from miss-firing (not knocking, they look the same but are very different).
Wrapping up about wot tuning:
The most important things to remember about tuning WOT:
1)No sharp peaks. Your torque curve should rise smoothly and taper off smoothly. If it doesn't ask yourself why.
Is your boost fluctuating? Is there a mechanical problem? Are you knocking? Are you near a knock threshold and need to leave some room on the table?
Horsepower is a mathematical relationship of torque over rpm. By knowing your horsepower you know how efficient your engine/tune is at that RPM point. ((Torque x RPM)divided by 5252=horsepower)
2)Your air/fuel ratio should remain flat. Pending what type of wideband sensors you shouldn't see much fluctuation. If you have a point where it suddenly goes lean and then back to commanded afr (say at 5000rpm you are 11.0a/f ratio, then at 5200rpm you jump to 11.6 a/f ratio and then at 5400 its back to 11.0 a/f ratio) you have a problem. Most likely that is an cylinder misfire, but it could be knock. Start buy pulling timing (safety versus sorry) or boost, see if it cleans up. Do it a few times (assuming you started aggressive on your wot tuning) and if it doesn't fix it, go the other way.
3)Since you are logging, you should have minimal knock count. If it does "knock" what does the car do? Does it make sense it is knocking? Does it ramp up smoothly, or spike?
Sometimes noise can be interpreted as knock, especially with modified engines.
Throttle tip in fueling should be handled well enough from the factory, same with decel (factory ecu should take care of all that). Your 02 sensors should keep you within check at part throttle conditions once you dial in your injectors, and timing shouldn't change much expect for peak power levels compared to factory.
My logical form of tuning:
1)Car mechanical sound
2)Make it start
3)Keep it running at 2000-3000rpm
4)Make it idle
5)Make it move under its own power
6)Part throttle tuning
7)WOT fuel/timing
8)Trims and corrections.
Questions/Comments/Concerns?
Did I miss anything on this?