Electrical problems, smoke, car dead.

5.0Gil - may need more info yet. Do you have a sig with descriptions of your mods? Fusible links don't go bad gradually - they either work or not. If you have the stock 65A alternator with a lot of elec. accessories (electric fan(s), stereo equipment, etc.) you may simply not be keeping up with the load - which is taxing the battery. If you have underdrive pulleys, they also slow the alternator down which may impact charging. You may also have a short (very low load) that's drawing the battery down slowly over time. Based on the info in your last post - sounds like something is interfering with charging. As jrichker alludes to - it ought to be up in the 13.8-14.4V range with engine running and no accessories on if the alternator output is healthy. If 11V is all you're getting, it sounds like the alternator isn't charging at all and it's just running off the battery - which will wear one out in a hurry.
 
Simple test:

Use a clamp on amp-meter.

With all accessories off and car at idle. Let run for 15 minutes
Clamp over the + battery wire (near the battery). Record the amp load.

Clamp over the wire that charges the battery (from the alternator). Record the amp load.

If the battery amp load is higher, your alt. is not producing a charge OR can not keep up with the total system load (and current is leaving the battery). In othe words, your running off your battery.

In theory the battery is only there to store energy for the starting motor. When engine running, the alt should handle all electrical loads (charging the battery, lights, radio, horn etc.) Once the battery is charged, it draws virtually no amps and hence the draw should be signifficantly lower than the alt wire.
 
No under drives, I'm running a alt from a Lincoln. It's a 100 amp alt( the old alt was doing the samething). I've had this problem for a while so may be it is a draw of some kind. Whatever it is the chime for the door dings real low and the radio light inside is so dim at night it's hard to see and during the day you can see off reflection. I have very little mods, ext. Mass Air, clutch. Wanna put in my 6AL-2 but afraid that the charging problems might kill the box. Thanks for your help.