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What kind of alarm was installed on the car? Is it a Honda alarm or an after market alarm (what brand)? If an after market alarm, do you have a valet switch? Please let me know, so I can further assist you. Thank you.
Do you have the remote start hooked up & working? Can you get the alarm to go into valet mode, then able to start the car? Did the no start condition happen after you installed alarm? Is the bypass, part of the alarm (Autopage) itself or separate from the alarm?
I think the bypass to the factory immobilizer may be causing the problems. But we'll see. Any other questions, please let me know. Thank you.
The key you will want not to use is the gray one, that is the valet key & not recommended to use if you are having these type of troubles. As long as the bypass is removed from the immobilizer, the car should start. Here is a diagram (Civic coupe, should be same for sedan) of the keys:
Look for pages 79-81 or pages 76-78. You should have a total of 3 keys. 2 with transponders & 1 valet key. I think also with the use of the after market alarm, your keys may have been to close to the immobilizer system, or multiple keys near it. If you have the 2nd transponder key, get that, with all of the after market alarm disconnected & see if the car will start. Also, you can try to disconnect the battery for approximately 10-15 minutes to try to reset the systems. Then try with only the transponder key to see if it will start. Last resort, may be taking to the dealer to have them reset & re-code keys. Let them know, you took it to a stereo shop & they could not get it to work. Honda will have a big issue with you installing it. You may be able to get it covered under a goodwill warranty. Please let me know, if you need sedan information or any other questions. Thank you.
From what I am finding, it says to try the keys, one at a time, till the key or keys are recognized. Keep all keys separate from one another while trying this. The immobilizer light should come on for about 2 seconds & either go off or start to blink. Not sure why it is not coming on. I would try one key at a time, hopefully is will sync up & start car. So with the alarm completely disconnected, are all the wires are the way you found them when you started? I did find some information on a Honda bypass module:
I'm not sure if that was very similar to what you were using. It shows 2 different modes & cutting wires. If you did not cut wires, how did you hook it up? If not, you are going to have to take to the dealer. Please let me know. Thank you.