Avoid cycling the ALT switch
The blast tube will help, but the alternator is running backwards from what it was designed to. When this one goes look at Plane Power. They are built with 2 cooling fans turning the correct way to cool.
http://www.plane-power.com/
I agree but all ND's have two internal fans, but you are right, they are running backwards.
14.1 volts sounds TOO low
The alternator you have should be set to 14.5 volts. The lower volts could be loss in wiring over distance, which is normal. 0.40 volts is a little too high. It could mean the alternator is not making spec volts. You could also have bad connections on your b-lead. Check the wires, connections and terminals. It is not uncommon to have a lose B-lead connection or bad crimp terminals. Lots of vibration going on. You expect some loss from the alternator to where you measure voltage but 0.40 volts is too much. You say it use to be normally 13.8 volts? That is way to low for the standard Suzuki Samurai ND alternator.
If your B-lead connections are poor or intermittent you can damage the alternator.
HEAT
A blast tube on the voltage regulator heat sink will help. Semiconductors service life and heat are directly proportional. Also back there are the rectifier diodes.
Also Consider a head shield off the back of the alternator or the #1 exhaust pipe. You don't want the Pipe and Alternator to have line of sight between each other. Infrared radiant heat will cook your alternator. It is not only the air temp but the radiant heat. It's like the warmth of the sun on your face on a cool day.
You should SHIELD the back of the alternator from nearby hot stuff, and the first foot or two of the #1 pipe is about as HOT as it gets.
Turning the Alternator ON and than OFF while running = sure fire way to kill your alternator NOW
I have been researching this for a few years. There is a direct correlation to alternator failure and cycling the ALT switch while it is running under load. Call it anecdotal evidence or scientific observation.
In a car you can't cycle the alternator with the engine running. The key and ignition switch takes care of the sequence of what goes on or off. The alternator is on before engine start. There are timers and logic in the alternator to start the alternator softly. You are defeating that start logic by cycling the alternator off/on while spinning at high RPM. Not all alternators are like this, but stock ND alternators made to OEM standards are.
These alternators are designed for cars with an ignition switch; there is no ALT switch in a car. The alternator is ON before start and OFF ofter the engine ignition is shut off. There are circuits inside the alternator to take care of "soft starting" the alterantor.
Most IR have logic control in the form of a small IC chip. This is true of ND alternators made to OEM standards. Some after market alternators might not adhere to all OEM standards, but good ones should. The chip that does the magic is very sophisticated but cost about $1.50. It has all the start and stop and fault logic. There is no reason for manufactures not to use these IC chips. Most do.
I think the damage is done when the pilot turns it back on. That surge or voltage spike fries the solid state switching. This is an educated guess. I have never got a voltage regulator tested after failure. If you ever have a bad regulator, send it to me. I'll send it off to a company to find out what failed.
Regardless of the failure mode, I have discussed this or read this scenario from at least 5 or 6 pilots. You make the 7th. It is possible your alternator was going bad before you cycled it, but alternator noise is not necessarily a sign of a bad alternator. It usually means bad grounds or connections. It can be a bad rectifier diode but the voltage was normal? Did the AUTO STORE tell you what was bad?
The alternator's IGN lead is a very low current "wake/sleep signal" that tells the alternator to come alive, get ready to run. It also tells it to sleep when you take your keys out of the ignition switch. Telling the alternator to sleep and wake again while running I theorize causes a surge and overloads the switching, which is not made to handle large spike. (ER) alternators have no internal logic and switching, the "ALT" switch controls the power to the regulator.
WHY cycle your alternator off/on while its running? Its not a criticism, just a question, WHY? If you want to know if the alternator is running look at your voltage meter. If you suspect your alternator is making noise, it is. Noise is sometimes a regulator/rectifier problem, but it mostly comes bad connections. Just change RPM. If you can hear a change in the whine/noise, you know its related to the alternator (or bad connections / grounds). Never cycle the alternator on and off capriciously is my suggestion. If the alternator is clearly malfunction than turn it off.
Removing the b-lead from the battery while running will kill the alternator just as fast.
If you have some kind of OV relay or a CB on the B-lead, don't cycle it to TEST it working under load.
This WILL KILL YOUR ALTERNATOR as well. This is well known, never run any alternator unless it is connected to a battery. People have been known to take the positive battery lead off their car while the car is running to "see if the alternator is working". This will damage the alternator. It's NOT a useful test of anything. Use a volt meter to test.
If your B-lead connections are poor or intermittent you can damage the alternator.
I can tell you many pilots I talked to, start their, "my alternator failed" story with:
"Well I turned the ALT switch off to see what would happen and than back on. Than the voltage ........ went low ...... (or) ...... went high."