Keep blowing alternators and battery is not charging, code 41

First of all, there is nothing you can do to cause the alternator to fail. There are no electronics inside it other than the standard six diodes. The only way the charging voltage can go too high is because the control wire is grounded, or the regulator is driving the alternator that hard. I suppose if the system is being run wide open and you continue driving like that, the diodes might become overheated and short, but even that is not common. They aren't meant to handle full output continuously.

You are correct that the voltage regulator lives inside the Engine Computer, and while that circuit can fail, that is very uncommon. What we need to do is determine if this is being caused by the regulator or that wire is grounded. Locate the two small terminals on the back of the alternator, and for convenience, you might want to clip a jumper lead to the control terminal, then to a voltmeter, so you can monitor that voltage. The two wires go through a small black plastic block, then come out on the two terminals. You can't look at the wire colors to figure out which terminal you need, but that is real easy to do with the voltmeter.

The engine must be running for this to be valid. Measure the voltages on those two terminals. On one you're going to find full battery voltage which is supposed to be between 13.75 and 14.75 volts. We want the other terminal. On that one, the lower the voltage there, the larger the difference, and the larger the electromagnetic field will be created. Under normal conditions, you'll typically find between around 4 - 11 volts. At 4 volts, the regulator is driving the alternator about as hard as possible to produce its maximum voltage and current. The clue we're looking for here is due to all the internal circuitry inside the computer, even if the voltage regulator circuit were to short, it is incapable of drawing the voltage down to much less than two volts. If you find 0 volts when the problem is occurring, that control wire is grounded somewhere between the alternator and the Engine Computer. If the regulator is shorted, there's still going to be some voltage on that wire.

Post what you find, then we can figure out where to go next.

Dandy. If you get the chance, to see what normal is, measure the voltage on those two smaller terminals on the back of the alternator. I'd be real interested in knowing what the control wire was at with the old computer.

Happy to hear you solved it.