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I had a car do this to me and it ended up being a pin hole in the fuel line it was big enough to draw air in but not leak out.
No chance that electric fuel pump is crapping out? How is it wired?
I agree with emac, the OP's descriptions, symptoms and testing are very confusing. Like, It cranks slowly, then cranks over. Does this mean it started? In the pics it appears that the electrical connections need to be cleaned especially when trying to diagnose a possible electrical problem, then we hear about about a loose wire. By cleaning the connections he might find a problem. What I see in the black melted wire pic is corrosion starting under the insulation.
What's the condition of the pos and neg battery cables? Is the pertronix red wire getting 12 volts? Is the coil internally resisted? If it is, is it getting 12 volts to the + side of the coil. Did you have these same symptoms, of cutting out, b4 the petronix was installed? I fought a pertronix problem for a couple of months last year on our boat. The symptoms were identical to the OP's. It would run for a while sputter and die. At first, we were sure we had a fuel problem. I'd fool with the carb and then it would start and run for a while. With me messing with the carb, it allowed time for the petronix unit to cool down. One time, It started and idled fine, but if we applied more fuel it would sputter and try to die, till we backed off the throttle. I was still sure it was a fuel problem so the next time out i brought another carb to swap. 30 mins into the ride the motor quit, we were getting ready to make the carb swap and noticed it was getting plenty of fuel, so we checked spark and had none. We pulled the petronix unit and reinstalled the points plate, and all is still good. I'd clean all your connections then start isolating various components of the ignition system. 1st if it has an internal resisted coil, disconnect the 40's pos wires off of the + side of the coil and supply 12 volts from the battery and start it and drive it. If the problems go away then its the petronix unit. Remember, to turn the engine off you'll have to pull that jumper bat wire off the coil. If the problem still exists, Id probably go to the next easiest component to isolate, the ING switch. Disconnect the switch's plug from the harness, locate the bat wire, ING wire, and start wire, in the 40's plug and make a pig tail so you can hot wire it and drive it. etc. There may be 2 separate issues going on, 1 slow cranking and the other stalling/cutting out.
It starts up just fine after it sits. Usually on the first or second rev. It starts the same way every morning too. I pump the gas twice and it fires up immediately.
I haven't poured gas into the carb. I mentioned earlier I've pulled the fuel line right at the carb right at shut off and dumped it into a bottle and keyed on the truck and got fuel flow.
Great information as now we know that you have fuel in the carb bowl when it won't run.
so now I see it as 3 possibilities
1:the one I lean towards is a vacuum leak thus gas in the carb not getting sucked into the intake. Can easily be determined with a vacuum gauge. specifically I still suspect intake to head as you have headers but won' now without testing.
2:Something heat related is messing up you timing. Easily checked with a timing light.
3:lastly in my mind is you have described how hot the engine compartment is and makes me wander if it is possible that this might be affecting the fuel that is in the carb. don't know if this even can happen while it is running - just thinking.
I honestly know more local people who have had problems with Pertronix ignitions than those who have not. The failures I have seen were fatal - the vehicle dies while running and never restarts. You may have a heat-related occasional failure in the module.
I would consider getting a spare module for the distributor and swapping that in. If it doesn't solve the issue, then you have a trail spare.
I have an import shop around the corner from me and while these guys don't specialize in FJ40s they have seen quite a few over the years. The owner thought it was fuel evaporating out of the Weber 38/38 I run. He said they have a small fuel bowl and heat from the manifold and header is making it evaporate.
He wanted me to wrap the header to abate heat.
I've also recently discovered this which I was unaware was even made. A carb heat shield:
You’re probably correct in the electrical thing since there was a change. On the vapor lock issue, however, when one has an aftermarket carb, non-OEM fuel line routing, non-OEM fuel pump type, and modern fuel blends, Mr T’s Engineers are off the hook. My truck was living proof....