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First off I'd like to say that tuning is a concept that cannot be tied to a single platform.
NA-T gets tuned the same way a TT does, and a TT gets tuned the same way a Honda does.
It also cannot be tied to any single tuning tool.
Some people believe that tuning with an SAFC is nothing like tuning with a VPC when in fact, both tools modify the Air Flow signal that goes into the ECU in order to manipulate the amount of fuel delivered.

Once you decide on a tool (usually based on HP goals and/or budget) the tuning concept is simple: Set a solid AFR under boost (most say 12:1 is a safe AFR to run but it depends on boost levels), then slowly advance timing and watch the power increase. As soon as you see power fall off and/or see detonation (knock), retard timing a bit and you’re where you want to be.
This is the reason why the dyno is recommended* for ignition tuning; you can see small changes in power output. Unless you were born with super-accurate lateral acceleration sensors in your peripheral system, you won’t be able to sense these small changes on your own.
Fuel can be taken care of using street tuning because fuel is mostly tweaked to improve driveability.

To answer the question about how to detect knock, conveniently enough, our cars came with 2 knock sensors, 1 front and 1 rear.
These produce a 0-5V+ output that can easily be logged with the datalogger of your choice.
The knock sensors are really microphones, so when your engine is at a higher RPM, you’re going to get ‘noise’ and the knock sensors are going to start outputting some voltage.
You have to learn the ‘noise’ your car makes without knock.
Best way to do this is to run your car through the RPM range (under load of course) with safe timing and some high octane gas that ensures you’re not knocking.
You’ll see what voltage the knock sensors produce at what RPM without any knock.

When you start datalogging (tuning), you’re watching out for voltage spikes above the voltage you measured in your ‘base’ run.
If you see spikes, retard timing until they’re gone.
Luckily the 2JZ engine is built very tough, and is quite forgiving when it comes to detonation.
By the time you see the knock sensor spike in a stock Civic motor, the internals are most likely destroyed.

*Although I cannot vouch for it personally, Innovate’s AuxBox has built-in lateral acceleration sensors which can be used instead of a dyno. The problem with this is doing a WOT to redline in 4th gear. If you live in the middle of nowhere, it can be done, but when I tried such a run here in the bay, I ended up with a very hefty fine.

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