[RICK LAKE]

iron head 3 problems, Lets start with charging system, How big is the Alt in amps? How many curcuits are pulling power when the car is running? Lights, electric fuel pump,Ignition box, ECU for FI system? If this happens at idle the Alt can't keep up with the load on the system. I am going to say that the battery is new and fully charged. It doesn't hurt to pull it and go and have it tested for loads and CCA rating. You could have a bad cell. Car will start and run but with things on like cooling fans they pull about 10-20 amps. At idle the charging system can't charge the battery. Ideas charging for a battery in voltage is 13.7-14.2 volts. As long as you are 12.7 volts and holding with all drains on you are ok. Anything less need to rework the system, see below.
3 possible fixes
1 Does your motor have March pulleys on it and are they underdriven? If YES need to go. The Alt is not spinning fast enough to keep both the battery and load getting enough ampage to system. The water pump and crankshaft pulley should be the same diameter. As for the ATL pulley size should have the stock pulley on it for a loaded opitioned truck or car. If not change pulleys first. If you have alot of curcuits running at idle, the battery will discharge trying to keep power going to every curcuit.
2 Output of Alt, in the old days we had only a couple of curcuits in a cobra. 37-42amp Alt was fine for this car. Today, multi fans, electrical fuel pumps, Ignition boxes, Better head lights, Stereos, and other power drainers. Need a higher power Alt in the 90+ ampage for the car to start everything and handle all the loads at idle. There should be a number on the ALT that said --amps. We are looking for 80 or higher. The Alt can be pulled and tested for output also. One of the diodes could be burnt out and cause a weak output on the ALT. OUtput should be within 5% of number on case. Less buy a new rebuilt Alt. There is a PROBLEM with running more than 70 amp ALT's. The Amp meter in the dash Can't handle this load over long periods of time. There are other threads about amp meters burning up dash harnesses, melting the insolators on the gauge and other problems. IF you are going with a higher output Alt than 60 amps, replace the Amp gauge with a voltage gauge. Works almost the same and you can chack the output of the charging system looking at the gauge. A simple rewiring from amp to volt is done. Will need to add a 125 fusible link to the output on the Alt for protection of the car incase of a short or rub through on the power side.
3 There could be something going bad with the coolant fan(s). Need to find out how much ampage they are drawing. When the fans kick on there is a ampage and voltage drop for a second. The gauge could pin and bounce back with them running. Other thing is a bad relay for the fans. These are easy to replace and might help lessen the spike load.
The bad thing with a cobra having a amp gauge all the loads go through it. There are only 2 terminal post and small nuts that handle this load. under 60 amps total no problems, over 60 amps, looking for a melt down over time. Either way replace this gauge. This should give you all the info you need to fix the charging system.
A place called PA preformance sells a complete kit to swap out to a bigger Alt leaves the voltage box and looks orginial in the car. This kit works great. I have it on my car as well as going to a voltage gauge. Good luck with problem. I think you will fix it. Rick L.