Did you test the new alternator while at the shop, to make sure that the new one works?
If not, then when you take it back, have them test it with your jig.
Did you ever confirm battery voltage on the Yellow w/white wire to the regulator?
Usually there is no fuse involved, when people connect it to the BAT output stud on the alternator. And originally there was no fuse from the factory.
Later models might have had a fuse, but I don't know about it.
So, you confirmed that your Green w/red wire has 12v with the key ON.
There is no connection for the White w/black wire on an Explorer 4G, so that should go nowhere on yours.
The Yellow wire needs battery voltage all the time.
Pull the plug and see if any of the contact points are bend or corroded. At the very least, confirm power with a volt-meter on the interior contacts.
Are the Explorer brackets painted or powder coated? If so, run a dedicated ground wire (a large one!) between the alternator case and the engine block, or battery negative.
Verify that you have a good body ground (a couple of them) still.
The grounds you absolutely should have:
1. Main cable to the engine block.
2. Smaller gauge, or a direct splice, from the negative to the body.
3. Smaller gauge (usually 10ga or a braided strap) from the engine to the body.
4. And of course, there absolutely needs to be a good connection between the alternator, any brackets, the engine block, and therefor the battery.
Don't think it would make a difference, but you know the belt is turning the alternator the correct direction? Again, probably does not matter. But it doesn't hurt to find out.
When you get a chance, post up some pics of your setup.
Paul