Sunday and Monday I made a road trip to ATL to pick up my tranny with the Bonneville. It ran like a top the whole way there, and while I was there. On the way back, I lost all power to the car for two or three seconds, but the engine never went out, so I drove cautiously to the next exit 1.5 miles away, and it did it once more on the off ramp, so I didn't even wait to get to a gas station. I pulled on the shoulder and started troubleshooting. The first thing I looked at was the alternator, had good connections. Next the battery, the positive terminal had melted, and one of the wires was just laying on the terminal. Below the battery it looked like a pile of melted and dried again solder. Is there a cause for this that I should worry about, I replaced the terminal at a nearby auto parts store. I am glad I carrried tools, because I almost didn't put them in the trunk.

BTW: The dumbass I bought the tranny from didn't bother to drain it, so now I have a spare tire well full of fluid, good thing I entirely stripped the trunk.

Yes, I would definitely be worried. This is a major high current evolution that took place. I would start by replacing the battery, all battery cables, bench check the alternator (load test it), and before restoring all the connections, take a good look at the electrical system. Do you know if the battery main terminals(+) & (-) were adequately tight prior to this happening? Any other unusual electrical faults before this? When was the last time battery was serviced?

The battery is fairly new and has good charge. The alternator is worn out, my stereo system has abused it. My car only run at approx 12.7 volts unless at a traffic light, then it dips into the 11s. Do you think thats what did it? For my motor swap I had the alternator beefed up to handle the extra load, would this fix the problem?

Ah HA! you are pulling major amounts of juice from the battery with your system. This could assist in the meltdown