If you measured 16V at the same place the #2 wire from the alternator was connected you MUST either have an alternator problem or a bad wiring problem (ground or power wiring). I just can't think of any other reason this won't work.
The #2 wire is the sensing wire for the alternator. That is the terminal that the internal regulator measures to adjust it's output. So, the voltage where the wire is connected should not go above the 14.2V that the regulator operates at. With a heavy load, you can draw the voltage down but it should never go above 14.2V at the point where that wire is connected.
What size of wire were you using when you connected the #2 wire to the other locations. The stock wiring harnesses I see have what looks like a 10 or 12 gauge wire connecting that terminal up. It must be heavy for a reason since the factory wouldn't waste the heavy wire for no reason.
Another thing to try is to move the meter -ve lead around when you're measuring the voltage. For example, when measuring at the same spot try putting the -ve wire on the body, frame, engine, alternator case, etc. The voltage should always measure the same or the ground is bad. Similarily, you can put the meter leads at each end of a wire to measure the voltage drop across it. Remember, every wire will have some voltage drop but with the wire sizes you have the voltage drops should be very small, likely in the 0.1 to 0.2 volt drop range as a maximum.
I think you need to eliminate a possible bad wiring connection. Crank it up with all the loads and look for a hot spot in the wiring because that'll indicate a poor connection.
If you are sure about the wiring then ask the alternator rebuilder about the #2 terminal being used as the sense wire and connecting it to another spot besides the bat post on the alternator. Maybe he did something funny in the rebuilding (what I wouldn't know). Maybe you need to take the car to him and confirm the wiring method you're using with him.
I can tell you one thing. If you want to run it with the #2 terminal connected to the Bat post on the alternator you will likely have to increase the wire size of the alternator to battery run and still live with a low voltage in the engine compartment. As an example, 8awg is 0.67 ohms of resistance per 1000 feet. So, 0.67 divided by 1000 is 0.00067 ohms per foot. 25 feet would be 0.01675 ohms. Times that by 90A and you get a 1.5V drop. Scary, huh? So, if you have 14.2V at the Bat post on the alternator the best you can get is 12.7V at the battery. You then get less after the wiring run back to the front of the car. By moving the sensing wire, the alternator will produce 15.7V at the Bat terminal so that you get 14.2 at the battery.
So you know, 1awg is 0.126 ohms per 1000 feet and 25 feet would have a 0.28V drop at 90A. So connecting the #2 terminal to the firewall end of the #1 wire should not result is a voltage at the battery much over about 14.5V.