As is usually the case, I am in agreement with everything Burns posted. For what it is worth, I thought I would answer some of your questions that were not specifically addressed.
Where do the black/orange-stripe and light green wires go?
You did not specify model year. On my '03, the black/orange is the main charging wire, and goes to the big lug on the back of the alternator, where the insulated spacer was removed. The light green wire is battery voltage sense, and goes to the 3-pin connector on the back of the alternator.
What does re-clocked mean?
It is a term commonly used by military techs to describe a change in angle. In your photo of the alternator (original post, 4th photo), the lug is bolted such that it exits the alternator at approximately 4 o'clock. The safe zone is between 10 and 11 o'clock. Any other angle risks a short to the alternator case, which is ground. In your image, the short looks to be there already . . . but pictures can be deceiving.
Where is the short?
The insulator/spacer limits the angle of the charging wire and spaces it a safe distance from the alternator frame.
To remove the insulator, did you have to remove both nuts on the stud, or just the outer one? If both had to be removed, you may need a fiber washer between the lower nut and alternator case to prevent a short.
Another possibility is the stud rotated during removal of the insulator/spacer, possibly causing a short to develop within the alternator. Finally, the insulation may have been compromised somewhere between alternator and battery positive, and the bare wire is coming into contact with ground.
How to prevent burning up another fusible link?
Do not reconnect the negative battery terminal until you know the short has been cleared. There are numerous methods to determine this. In my opinion, the safest is a "low tech" test light. At a wrecking yard or parts store, buy a brake lamp socket with wires, and a brake light bulb to fit in it. These bulbs are usually 21 watts and will draw about 1.5 Amp. Strip about 1/2" of insulation from the free ends of both socket wires. With the ignition off, hold one socket wire in contact with the negative battery terminal and the other to the (still removed) negative battery cable. If the lamp lights to full brightness (touch the socket between + and - battery terminals to get an idea of how bright that is), the short is still there. If the lamp lights more dimly, you have less than 1.5A of ground current, meaning the short has been cleared.
If you get a bright lamp, remove the big lug from the alternator, and try again. If the short still remains, inspect the entire length of the charging cable for damaged insulation near or in contact with a ground.
Report back, and Burns or I will try to guide you from there.
