1989 Ford F250 7.3L Diesel. Bat light came on then smoked the VR

The first thing to do is have a fault code test run on the engine control module.

Is this E-150 econoline?
Engine running, take reading at generator bat terminal, what is it? The basics, take reading across battery terminals, everything off. Take second reading at bat terminals, engine running. The second reading should be higher than the first if charging system is working. Was the charging system checked on the vehicle when the generator was checked out?
There could be a wiring circuit problem? The bat terminal at generator is hot all the time, engine running or off.

follow hot cable form bat right to starter

You may have a a/c voltage leak comming from the alternator..If its a rebuilt alternator sometimes you get a bad one ..But make sure all your connections are good ecspecially the small wires coming out the back ..These are the field and sensor wires..Plus make sure all your grounds on the vehicle are not broken or missing..You can have good voltage but it may have a drop going to the computer because of a ground and cause the light to come on

1989 f250 4x4 lighting problems. i replaced the floor mounted dimmer switch ,the lights worked fine for an hour untill i turned them off.Now the lights will not turn back on but i have park lights.

find the horn and tap it with something sounds like its stuck

insert key turn to on position alarm should silence
once bat conected start truck

So I assume you never disconnected the bat. when changing the coil that is not good ....I would say buy another coil pack and start over and make sure to disconnect the bat.......Check all wires going to the coil for breaks or worn or burnt marks in wires before hooking up new coil

sounds like alt. wasn't charging/or bat wasn't taking charge. take bat to have tasted. if its ok. suspect the alt. with a good bat. the voltage at terminals when running with lights on should be 12-14.5.

This makes me think that there is a problem with the ignition switch. It sounds like it is making the connection for the truck to run when it is in the "on" position, but not when it is in the "start" position.