So alt com duty cycle is checked and the ECM is out putting 40% duty cycle, 4,95 Volts measured at the alternator ( a little low, but due to resistance in wires i guess its okay) this should output 13,4 Volts, but only 12,1 volts measured at battery posts. A little corrosion found on the frame ground post, but no resistance can be measured but will clean anyway. Next is to check the error state if it will output 13,8Volts with connector unplugged.

 

Three pin connector has now been unplugged and engine started. No Voltage output from alternator, so the brand new bosch alternator is pronounced dead. Ill update when new denso alternator is installed. What killed the bosh generator i think is the high voltage in start up wich appears to be too much for the rectifier maybe its connected with the AGM battery. It seems that the OEM is designed to handle these high peaks.

 

Did you replace the ground wire from the body to the battery? (the one that goes back up under the fender).
We know that a bad alternator will make the cooling fan run non-stop, but you may want to look at the coolant temp sensor as it also controls the cooling fan. Are you having any HVAC issues? Do the temp ***** make the air hot and cold? HVAC affects the cooling fan as well.

Also the voltage spike may be an effort on the alternators part to charge the battery, and with a bad ground cable well....... it won't operate as expected.

Hope this helps
Jeff