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My guess is batteries. The PCM needs 10.5 volts to start the truck. When it drops below that during cranking, it will often click under the dash.
Of course none of this explains why the clicking will stop after some cranking and then start. I cannot imagine the batteries getting stronger the longer you crank, perhaps the fuel pump timer going off leaves the batteries just enough juice to get there.
Since it is summer, may want to disable the GP relay lead from the battery, and try cranking it to see if the clicking goes away and the truck will start.
Like ZX, Kwikk, and Tenn said, change the batts(trust us), I have had this problem before. I also could not believe that my 6month old batts could be bad.
I was wrong. they were bad as well as my alternator. start with two new batts, crank it, drive to local auto parts store and have alternator checked.
The clicking is the GEM (VSM) after you try to crank it a while (with clicking) do the interior lights and hazards start flashing ?
Well, you guys were right! I took my 25th aniversary gift from work and bought a Fluke multimeter and tested the battery cranking voltage. It was 8.7 to 9.2 volts. so, I replaced the two batteries with two known good ones and the truck started like a champ. My theory of what was happening is as follows: With the original, on its last legs starter, the starter resistance was so high that it was drawing less current, causing the battery terminal voltage to remain high enough to start the truck. When I replaced the starter, the current draw went up drastically, reducing the terminal voltage on the battery as the starter spun the engine much faster, fooling me into thinking the batteries were good. After prolonged cranking the terminal voltage would decrease, slowing the starter and lowering its current draw which in turn would allow the battery voltage to rise to the magic 10.5 volts needed for the computer to fire the injectors. I'm guessing on the last one, perhaps the glow plug load was also playing a part, since the truck did usually start better when warm. Anyhow, all seems to be fine with the different batteries. Tomorrow I will go out and buy two new ones. Those batteries were in the truck when I got it, so I have no idea how old they are. I have no reason to suspect the alternator wasn't charging them properly as I had the problem even after putting a fresh charge on the batteries overnight. Thanks again for all your help.
alternator may have been charging just fine, but if its trying to charge a batt with a bad cell it can lead to a blown diode in the alt. Thats why I suggested having it checked after you replaced the batts.
Again you folks are right on. I took my new multimeter and checked the alternator. Although it was charging slightly (about 13.11 vdc) it had a bad diode. have to say that is the easiest alternator to change that I have ever done, and I've done a few in my day. Thanks to everyone who responded.