Strange Electrical Startup Charge sequence
 

So I got my 92 Club Cab back from body and paint 2-3 weeks ago. Stock no engine mods whatsoever. 161K on odometer but estimate prolly 275k by now. Shop owner said never any problem starting while he had it from April thru December. Before I took it to him the truck would start fine but the grid heaters would come on no matter the outside temp, cycle of and on till the engine warmed. When I got truck back I noticed driving down road to take it home that it was not charging. figured it was possibly alternator or something from peculiar goings on before it went to body shop. Body shop didn't tighten battery cables on inspection of ECM and all from replacing fenders and wells. Problem solved. NOPE! Had to boost it off. But now it cranks fine. Still does not show charge initially, but after its running prolly 5 mins the wait to start light starts flickering faintly and then the water in fuel faintly flickers along with the check engine light on the gauge. Once they all three start to shine bright you can here change in engine tone and the charge gauge jumps to 13-14 volts. All warning lights go out. Alternator was replaced Oct 2016, when other charging issue happened. Alternator had cracked housing. I have another ECM from salvage truck, but it's condition is unknown. Any help or knowledge appreciated!

Go through all the body to harness connections ( grounds ), cleaning, then reassemble. Clean batt cables, both ends. Including starter solenoid wire. Add extra grounds to body to block to battery. . all this to start. If no change, more to follow

Oh yeah. Pictures of your new paint job required

To be clear, remove all the paint at the ground point. You want metal to metal contact. Also use copper anti-seize between the terminal and ground. It will keep the connection from oxidizing over time.

Cougar... do you hafta use copper never seize? I have the aluminum/gray kind ... never thought about putting never seize on batteries terminals... would diaelectric grease do the same?? I always touch the tip of dipstick to each post and the one little drop of oil seems to cut down on the corrosion BUT there is oil stain on battery top and that collects dirt badly

The standard gray never seize is mostly comprised of graphite, which doesn't conduct current. The higher dollar never seize is nickel based. Thentheres copper based. None of them conduct current extremely well, as you can test it yourself with a multimeter. Dielectric grease works great, but requires frequent maintenance because with heat it melts, and attracts dirt.

I wouldn't use anything on battery terminals between the post and cable end. I do, however coat them with a protectant once they are cleaned, reasssembled and tightened, some people paint them to seal oxygen out of the top connection, but there are battery specific coating available.

Added photos original post.

Not likely your problem, but a dirty battery surface can create a small battery drain just like an underhood light. I would clean them up. I beleive your problem is directly related to poor grounding at one or more locations.

......

https://cimg0.ibsrv.net/gimg/www.die...f785b2bd37.jpg
https://cimg1.ibsrv.net/gimg/www.die...7fda162f72.jpg
https://cimg2.ibsrv.net/gimg/www.die...5f589d68ff.jpg
https://cimg4.ibsrv.net/gimg/www.die...42c7bb60c1.jpg

One of my trucks started doing that when it's very cold. When the wait to start light is flickering, I can hear a relay buzzing. I found that slapping the left fender would make it wake up and cycle properly.
I figure the ASD relay or it's connections is probably flaky. All things PCM, plus the alternator rely on that relay to operate.

Of course it could also be a ground connection, but it doesn't cost much to throw any mini-ISO relay you have laying around in the clip and see if it solves the problem.