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Don't worry about the program, it will have to be changed anyway.
Use a computer that will "talk" to all of the sensors that your using.
The injection system should be the same parts, the spark timing should be the same parts. The DOD/AFM can be programmed out if you use that computer.
then use the wiring harness that goes with the computer and the engine.
you may even find the 2 computers are the same part number, just different programs.
 

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With a bit of a cam and probably a little extra displacement, you might need to upsize the injectors; but they may be fine if the program just keeps them open a little longer.
 

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I'm sorry, I have a hard time trying to follow you.
Your last post has a 2008 truck and a 2004 motor,
You first post has a 2014 truck and a 2002 motor.
And in the other thread, you have a newer truck and an '04 motor

I saw your other thread, other than perhaps the physical shape, most Accelerator Position Sensors work the same. You should be able to use the one designed for the truck.
 

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You should have cleared that up, the '08 is very similar to the '04, the '14 is miles apart.

It it was me, I'd use the '08 wiring and make the new engine work with the wiring. You need to have the AFM removed from the computer. You also need a throttle body for the '08, so the Throttle Position Sensor is compatible to the APS

EDIT:
Note that I have changed my advice from an earlier post; at that time, I thought you were trying to put the motor into a 2014 truck, that's a big job. Putting the motor into a 2008 is less of a challenge..
 

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You are a member, you should be able to upload pictures.

Here is where I am. Most people do not have the documentation, tools or the skill set to reconfigure the truck's electrical circuits.
Use the parts and the wiring that came with the truck.
Convert the mechanical and the electro-mechanical parts of the old motor to work with the newer truck.
Reprogram the PCM to remove any sensors, or functions that you are unable to duplicate

In other words:
  • keep the factory wiring,
  • keep the factory PCM
  • add functional to the motor (additional sensors where possible, an '08 throttle body and intake
  • program remove, from the PCM, sensors and functions that you can not provide (AFM for example)
 

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You gave me the impression both engines were LS engines.
If that is so, both engines have and need position sensors. The wiring should be the same.
 

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Btw, the crank position sensor is not there because of AFM/DOD.
AFM is possible because there is a CPS.

The CPS is there to tell the computer where the crank is in it's 360 degree rotation. The CPS is the timing mechanism for the engine.
 

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There is and I have forgotten how to tell one from the other
 

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When I looked into my building I learned that the newer Gen has more teeth on that sensor where my truck is the old style it has I think 24 tooth I could look back at the emails and see but this is a 24 tooth block that I'm trying to make run in is it 52 tooth body
I could be wrong, but I think the LS engines are 24 teeth, except for the marine versions which may be 48 teeth.
The LT engines may have 24 teeth and 58 teeth
 

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Actually, it's not the sensor that has the teeth, the teeth are on a reluctor wheel, the sensor just reads the teeth speed, converting to pulses
 

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I could be wrong, but I think the LS engines are 24 teeth, except for the marine versions which may be 48 teeth.
The LT engines may have 24 teeth and 48 teeth
As I said, I could be wrong and I am.
Here is a Motor trend story and it tells you how to ID:

 

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Ok, I'm getting a little frustrated, did you read the link?
It tells you there are 2 sensors and that one is black and one is gray
 

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Ok, all that considered, check the colour of the sensors, if they are the same colour the wheels are the same number of teeth.
 

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Ok, I'm taking a break, I suggest you re-read everything that's been typed.
 

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I have and read the article I didn't see the wire colors in it but I see ur point if they are the same odds are they are same tooth I will probably read that article 10 times before I decide to cut wires or preferably switch sensors as I have the blown motor I'm going to pull the starter again and go from there
It's not the wire colour, it's the colour of the plastic case of the sensor:

One easy way to tell which reluctor wheel you have is to look at the crankshaft sensor. If it’s black you have a 24x wheel; if the sensor is gray then you have a 58x wheel. Also, for the most part, 24x engines will have a camshaft sensor just behind the intake manifold while 58x engines typically have the cam sensor in the front timing cover.
 
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