Chances are the battery is bad, or at the least severely discharged, both of them.
A couple of problems, the alternator is primarily designed to maintain charge in the battery as power is consumed by the vehicle.
It is NOT intended to charge a dead or defective battery! Doing so is an open opportunity to damage the alternator or the electrical system (as in the smoking amp meter connection).
Hopefully the alternator is not damaged. The amp meter will need to be looked at, could have damaged the meter or the connection. It may be working now, but soon the damaged connection will begin to loosen, corrode, and cause problems later on, about the time you forget about it being overheated, and you'll spend hours looking for the electrical Gremlin! LOL
The solution is to inspect and repair the amp meter connection, replace the amp meter if any doubt. Charge the batteries, have them load tested. If they pass, slow charge them to full charge, try again. Start the engine, bring the RPM up, check the voltage across the battery. It should run around 15 volts max. If above that, it is overcharging, if below around 14 it is under/not charging.
And please don't be disconnecting the battery while it is running! Dangerous to your health (as in an explosion!) and can damage electrical components, especially any electronics, including the alternator, regulator, ignition system, computers, or solid state accessories.
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Today's Featured Article - Talk of the Town: The Saga of Grandpa's Tractor - by The following saga is from the Tractor Talk Discussion Forum. Someone. The saga starts with the following message: Hey guys I have a decision to make. I know what you all will probably suggest and it will probably agree with me way down inside, but here it is. I have a picture blown up and framed in my "tractor room" of a Farmall M. It was my Grandpa's tractor, of which whom I never got to meet. He froze to death getting this tractor out of the barn to pull a truck out of the ditch before I was born. Anyway my dad and aunt had to sell it at the auction,
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