Thanks for this post. I have an '86 F-250 Supercab, 6.9, with some similar issues. Haven't ever noticed pulsing lights, but, then, I seldom, if ever, drive in the dark, either. Don't want to hijack the thread, so Mods feel free to kick this or open new thread.
I just replaced glow plugs, adding pushbutton for pre-heating. He still hates first-start, though. Once I've gotten him running first-time of the day, no problem. But, apparently, he's not a morning person. Lol. I'm not sure coffee into the intake will help, but not opposed to trying, I suppose.
My other issue is the one that drives me a little nuts. He has an after-market cluster installed just below the dash with charging, oil pressure, and temp gauges. Once started, charging gauge needle pegs to left side of the gauge, and only reads correctly after I turn on headlights. I suspect a ground problem, also, but it appears that my wiring behind the dash may have been done by the same guy as OP. In other words, it's a rat's nest. I've had the truck going on six years, and drive it with no electrical problems, other than the aforementioned gauge anamoly.
I'm admittedly not a gearhead, should have spent more time under the hood with my Dad, but any help Will be greatly appreciated.
Thanks. Be well.