Consider this: You don't need an alternator at all to run. If your battery is healthy your truck should be able to drive at least 50 miles without all the accessories on. My FJ60 recently drove over 100 miles and still started fine after I discovered the alternator wasn't charging as it should....even ended up driving about 25 miles with the headlights on and didn't stall.
So Alternator issues do cause problems but you have a battery for a reason. The battery is your power reservoir and it will run a car....even a modern car for quite a long time if the alternator has died. The only thing I think is happening with your alternator is that you are putting a load on it and a loaded alternator gets harder to turn and requires more horsepower. It sounds a lot like your fuel system isn't compensating for your various loads on the engine and thats causing a stall. This could be due to an unfound vacuum leak or a bad sensor, a dirty ground, or one of your main EFI components going bad...due to age, cleanliness, etc.
Alternators usually fail due to the brushes i the voltage regulator wearing out and or the contact surfaces the brushes riding on wearing. At which point the alternator stops charging or intermittently charges. I am sure that windings do fail now and then but I can honestly say that it the 27 years I have worked on and been around cars I have never seen an alternator fail due to a winding issue. Also if you are seeing 12.8v at idle with all the accessories on and over 13v with none on then you your alternator is charging fine. if you had a bad winding you wouldn't be seeing that.
"From what I understand extra load from lights and windows shouldn't cause the efi to bump up rpms because there is no extra load from the alt. The alt just has a constant torque needed and doesn't go up or down like when the AC kicks on. I may be wrong but even on carbed engines there is no compensator for loads being put on the Alt. Its the voltage regulator that tells the alt to put out more volts, because alts are supposed to keep around 14.2 volts no mater what rpm. "
I can assure you that when you put more load on the alternator the amount of torque needed to turn it does increase. A carbed engine will react to the increased load and the carb will do its best to maintain its idle speed but often the idle speed will in fact drop due to alternator loading if there is no other idle up switch. Alternators are not designed to output 14.2 volts regardless of the rpm. They are are designed to output max voltage at a certain rpm and if that rpm is say 2000 rpm you are not going to see 14v at idle
