It's most common to first work on AFR, and at times it can be pretty beneficial. If a car is too "rich" (too much fuel), it can bog down, make less power, waste fuel, and foul components. If you "lean" out the car (take fuel out) it's most common to see some power gains from this, and many NA car tuners will go at this. Some big-power Turbo cars will not be leaned out to the bloody edge though, as fuel acts like a buffer to prevent detonation. It tends to run "cooler" temps, and has a greater margin of error depending even on if you get a bad tank of fuel from a station. You're better to err on the rich side, as you'll be more likely just to "foul" plugs or O2 sensors, where as running too lean will more likely cause catastrophic engine failure, as detonation is not a good thing. If you're not leaned out enough to cause quick damage, you'll notice your plugs and possibly walls and pistons speckled with hot-spots. As everyone knows, it's a controlled explosion/burn in the cylinder, but when you get massive hot spots, the mixture sprayed into there can end up detonating when it's not supposed to prematurely like when the piston isn't in position to recess and instead it blows as it's just on it's way up, which can = $$$$ repairs.
Timing can make power too. It's just more common to do this once you're running new cams with a different profile, with cam gears. And usually, USUALLY it's done at the same time or after AFR is tweaked. This is something that you should really have a pro do, and not just say, "i'll throw a couple degrees here, take a few there, and see how it goes".
VTEC controllers are a scary thing as well at times. People don't realize it but you can have it engage too soon and it'll then, or eventually cause engine damage. My friend swapped a B18C into his Civic DX and he read the wrong stuff on the net, and after a few weeks he ran into problems. Now, companies like Hondata research all of this. If they have piggy-backs or flashes that do this you can be sure it's more likely in the safe zone for it.