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what wire harness did you change and why
I would get a full charge on the battery and go from there
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was your harness plug and play or did you splice wires?
I would do a factory reset charge the battery to full capacity and try again, do you have access to a scanner that would be able to get into the pcm?
You remove the negative cable let it sit for 30 mins and before reconnecting it touch it to the positive side and that should drain the system and all voltage in it.
no that does a simple reprogram on the computer and it should relearn after you get it started if that is the case.
also how are you bypassing and getting it to start?
Is this the original key that came with the car? the red light would indicate that the key is not programed to the vehicle
At this point I would think the car would need to be reprogramed, ill see if we can get a second opinion from one of the other honda techs,