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I've seen that happen on an a neighbor's 98 after the battery was disconnected and then reconnected. Engine didn't run properly, and lots (!) of trouble codes. Car was flat-bedded to dealer. Mechanic used the Subaru code reader (SSMIII) to clear the codes, and all was back to normal. The codes were caused by some sort of software glitch when the battery was disconnected and reconnected, and not due to actual engine problems. They included codes that would normally put the engine into "failsafe" mode. By clearing them using the SSMIII (not by disconnecting the battery), the engine control module starts back with it's defaults, instead of with the codes already triggered, and goes from there. Not sure if this is the same with your car, but perhaps worth trying.
 

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Battery, when fully charged, should be at around 12.7 Volts. 12.0 is usually a partially discharged battery. But the 14 V running is good. It's possible the battery has a bad cell, and can't be charged fully, or perhaps, as you noted, it never has a chance to be fully charged given the short commutes. It might be best to use a charger to get it up to full charge, or at least see if it can be charged.

The range of different, and seemingly unrelated, codes suggests they aren't real but are affecting the way the engine is controlled. They should be cleared, and then see what happens. If there is a real fault, one or more will come back. Otherwise the engine will probably settle down to normal operation.

P0101 Mass Air Flow (MAF) Circuit Range/Performance Problem
P0301 Cylinder #1 Misfire Detected
P0302 Cylinder #2 Misfire Detected
P0341 Camshaft Position Sensor Circuit Range/Performance
P0601 Internal Control Module Memory Check Sum Error
P1100 Starter Switch Circuit Malfunction
P1107 Secondary air injection (AIR) diagnosis solenoid - circuit malfunction
P1120 Starter Switch High Input
P1141 Mass Air Flow Sensor Circuit High Input

Although I imagine the code readers that Autozone uses can clear codes, I understand some stores won't clear codes on request. But maybe your local one will. Otherwise, many reasonable cost OBD-II code readers can clear codes and are often on sale at stores and on sites such as eBay.
 

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Good news. Thanks for the update.

Did Autozone clear the codes for you, and if not, how did you clear them?

Incidentally, your analog meter is fine for general work, but perhaps consider adding a digital multi-meter. They're relatively inexpensive, and will usually have the appropriate ranges for automotive work, including a low Voltage range that can be used to detect bad grounds in the charging system. Well worth it if you're going to be maintaining your car yourself.
 
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