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Hello and thank you for your question,Can you tell me what your working on please, year, make and model?
So your saying the new alternator is not charging the battery?
The alternator is controlled by the duty cycle from the PCM (computer) . Are you able to do some testing on the new alternator as well as the circuit from it to the PCM ?
Okay will to avoid replacing any unneeded parts some testing needs to be done, do you have someone that can help you do the testing?
Have them run the enclosed test, copy and paste the link toy our browser to open and view it.https://dl.dropboxusercontent.com/u/104923897/ALternator%20Mar%208.pdfPlease take a moment to rate my service so I can get credit for my time, the question remains open for follow up even after doing so, all you need to do is return to this question if need be.Thank you again.