You are the victim of some misinformation. The people at the auto parts stores are not mechanics. They understand selling stuff that is often not needed. The testing they are referring to with the Check Engine light has to do with diagnostic fault codes that can be stored in the Engine Computer when it detects a problem. They will read those codes for you for free, but you must understand there are well over 2,000 potential fault codes, and only half of them will cause the Check Engine light to turn on. Those are the ones related to something that could adversely affect emissions. That means there can be one of more than a thousand codes stored when the Check Engine light is not on. It is not correct to say the Check Engine light has to be on to check for fault codes.
The next issue is you need the charging system tested. That usually has nothing to do with the Check Engine light and fault codes. A charging system problem can result in the Engine Computer detecting a problem related to low system voltage, and that can set a fault code, but it is still the charging system that has the defect.
Most auto parts stores have generator and starter test benches, but those are by far the least desirable way to test those items. Starters need to be tested under load while trying to crank an engine. Generators need around five horsepower to spin them under full load, and no test bench has a motor big enough to do that. Testing generators on the car includes all the related circuitry in the tests. The circuitry is responsible for just as many problems as the generator itself.
Your voltage regulator is built into the generator so you got a new one when you bought the replacement generator. The issue here is a defective voltage regulator almost always causes a total failure to charge, or an over-charge condition, and both problems are rarely intermittent. The flickering you described is usually the result of the voltage regulator responding to something that is causing rapidly rising and falling system voltage, and that is not going to show up on charging system tests. For this type of problem you need to try various solutions while the engine is running and the problem is occurring.
I should back up a minute and suggest you have the charging system load tested by your mechanic. We need to see the results of the "full-load output current test". During that test, which only lasts a few seconds, the generator will develop its maximum rated current or exactly one third of that. A typical generator for a '98 model might be a 90-amp unit. If all you can get is 30 amp's from it, there is a failed diode inside it. 30 amp's is not enough to run the entire electrical system under all conditions. The battery will have to make up the difference until it slowly runs down over days or weeks. More importantly, the output voltage will be bouncing up and down a lot, and the voltage regulator will react to those "dropouts". The result you might see is flickering lights.
If the output test is okay, look for ground wires with loose or rusty connections. One of them goes from the battery negative cable to the body sheet metal. On some engines there is another one between the generator and the engine block.
Thursday, September 1st, 2016 AT 8:48 PM