After Saturdays starter/battery wire fire problem my car has developed a charging problem. The car will start, will show a positive charge, then all of a sudden after a couple of minutes will go into a negative charge position and die out. The car battery is then completely dead. As far as we can tell the only physical damage was to the lower part of the starter wiring harness. Thankfully that was all. Could the positive cable from the battery which came loose and caused the fire by making contact with the starter heater shield, caused an electrical spike somewhere else in the car ? prior to this the car was running excellent. The alt has less than 500 miles as well as the optima battery. Any idea's ?

Either the alt is bad, such as a blown diode-trio, a shorted wire, etc., or there is a wire somewhere that melted when the starter went up in flames. You have a MAJOR short somewhere, to kill the engine in just a few minutes.
Try this...unplug the alt, and take the pos. cable off of it.(make sure the batt. is fully charged) Put a voltmeter on the batt., start the car, and see if it dies in a few minutes. If it does not die, then you have an alt problem, or something in the wiring from the alt to the batt. is amiss. If it does, make sure you have a fire extinguisher handy!! If there is a large enough short to kill a good batt. in just a few minutes, it will eventually let all of the smoke out of the wires.
Are you sure your batt. is still in good condition? If it has a shorted cell in it, it may be enough to cause this, but doubtful.

Joel we're in the process of trouble shooting. I must agree I think it's a major short that developed somewhere. As I stated earlier, the car shut down on me last night, I had the trickle charger on it all night and still the batt was totally dead. I must have been feeding a drain in the system. Thanks for your help and I'll keep you guys posted.

Octavio, are you disconnecting the batt. while charging it? If you are, and it is still dead after charging overnite, I'd be looking for a replacement!!! If not, then you are definitely trying to charge a short!!

I suggest a quick dis-connect for the batt. It will save yer butt if it ever does completely short out while you're not around!! Well worth the few dollars!!

I'm keeping my fingers crossed, but by Jove, I believe we got it . There was a starter ground wire that was fused to a hot wire. Even though the wire harness was pretty much redone, that rascal slipped by. The alternator diode was also bad, which was redone as well. As of right now, the car is running great and everything is in working order.  Thanks to all for your great advice

Atta Boy!!! Great news, 'bird!!