Need Help!!!!!!!!!!!!

I just picked up an 89 Gt. The car was sitting a year, and when we finished putting it back together all it needed was a new battery and it fired right up. Two days later the car would not start. I measured the battery, and it was completely dead. So I asked my neighbor to jump it. As soon as we hooked up the jumper cables one of the wires coming off the starter relay started smoking and burnt up. If I traced the wire right, it splits into two wires, one goes to the alternator, and the other goes to the voltage regulator on the alternator. What could cause this, and what can I do to get it fixed ASAP?

ok this is what I did. I found out that the fusibale link will blow if there is a bad ground on the battery. I put a new ground cable in, cut the fusible links out and put a normal fuse is place. Now, if jumped the car will start and run fine, but the battery will not hold a good enough charge to restart. How many amps does the alternator need to recharge the battery? I have a 15 amp fuse in there right now, but is it enough to charge the battery?