Most intake systems will not affect the air fuel ratio in a way that will harm the engine. However this does not mean you will get an optimum ratio so you won't get as much horsepwoer because it will be a slightly lean mixture. You do not have to flash the ECU and there is not a flash that will take care of just the air fuel ration.
There are 2 kinds of intakes, cold air and warm air. Cold air takes air from outside the engine compartment and can, depending on design, allow water in the intake if you live in area where it rains a lot and flash floods. Warm air intakes take air form inside the engine compartment and therefore do not have this problem and are only 1 or 2 horsepwer less at best. There is a company called, INJEN that makes intakes that are tested not to affect the air fuel ratio in an adverse way. However if you want the best horsepwower there is only one real way to set up a cold air intake. First if you don't have anexhaust that is free flowing, aftermarket poerformance, you won't get much out of the intake. If you do get an intake however, you need to get an air/fuel ratio or wideband oxygen sensor and gauge setup. They can be had for under $200. Then you need an adjustable fuel pressure regulator and fuel pressure gauge. The stoichemetric ratio is 14 to1 which gives best econlomy and power but to get real performance 12 to 1 is best. The adjustable regulator will cost under $100 with a gauge maybe a little over. Some are more expensive but for your application you don't need an expensive one. Edelbrock makes a good one andAeromotive makes high end ones that are expensive.
If you want more information go to http://www.carrepairlinks.com and look for performance retailers that will carry aftermarket parts for your car. I believe Horsepwoer freaks or CARiD would be best. Going through carreparlinks will oftne get you a discount on your order just for being a reader. The best tech advice would probably come from hjorsepower freaks as they are enthusiasts as well. They do have a discount sale going on till the end of spetember and may have some clearance parts for your application.

Answered by DrCranknWrench (expert)
3,292 answers provided