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Hey Guys I almost done with my swap did everything including groundin out wires and everything inclusive got my key flashed with Manual ECU.. Problem is that when I turn key to start the car it cranks over but does not start and there is unusual clicking noise coming from the glove compartment area. My friend told me it might be a relay or something...help me out here??

 
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sounds like the PGM Main relay number 2 for the fuel pump. somethng like that.

 
Rep Power: 228

Did you remember to reconnect the important ground wire on the thermostat housing.

Does the fuel pump prime?

Is there spark at all four plugs?

 
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no sparks on plugs

 
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The more information you give, the better.

Does the fuel pump also fail to prime?

Any CEL codes?

Did you check the thermostat ground?

 
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The fuel pump is good double checked the ground...There is no unusual icons that pop up on cluster...My friend said he is going to hook up a scanner to check... I will try to record a video and post it up

 
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ok so here's what I got

1) your fuel pump is good
2) you are getting the required volts
3) your not getting a code.
4) and most important you not getting spark.

Well first you need to check your ignition system. the ignition system goes like this

Spark plugs------>Coil packs------->PCM.

The bad news is that if your spark plugs are not working MY GUESS is that your PCM **** itself or maybe a fuss if there is one for the ignition system. The only reason why I say that is that I had close to the same problem..... $700+ later It ended up being my PCM.

I replaced my spark plugs, intake filter, All coil packs, fuel pump and then the PCM
I got the PCM off of ebay and then towed it to Honda iwth a friends truck where they charged me like $80 to reprogram imobilizer.

 
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IMMOBILZER**
I took my car to dealer to flash key..They might of messed up or something with the immobilizer...or the ECU I got is messed up..Because b4 flashing key...Green key icon shows up wen opening switch..
Now after flashing key it doesnt blinks wen switch is open But, When I try to start/crank engine it green key icon blinks. What should I do get a new ECU?

 
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take it to te dealership and have them reprogram the ECU with the IMMOBILZER. Imobilzer has to be sync'd with the keys and the ecu I think. I had to when I replaced my ECU.

 
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I'm having the exact same problem! i get the clicking from the glove box but the car wont start. i change the motor the other day i didnt change the ECU tho. my car is a 01 ex with manual. it has ran fine for the past 4 days but this moring on the way to work it cut off all the gauges went down and it wouldnt start back. i hear the clicking from the glove box. but get this if i unhook the battery cable for a minute and hook it back the car will start and run for a few minutes then it dies again? could it be the immobalizer?????????????

 
Rep Power: 228

Have the battery checked.

 
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battery is putting out 12.3v so it aint the battery someone told me it might be the main relay

 
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I had the same issue. I had to change my ECU good luck lol.

 
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well i changed the cam sensor, and got it running now. but it doesnt idle right
i had this problem before it stopped running. the idle jumps up and down from 1200 rpms to 2000rpms. i cant remember the code that came up, think it said idle control malf. any ideas?