1. I got this.
2. Not sure if I got this, but I think the answer is YES.
The stock alternator cable is unusable for the 3G, it is way too small. You have to add a 4AWG wire to replace it, not supplement it.
From the link I gave you, these are the important things:
DO NOT remove the existing 10AWG black/orange wire (connects to a green fuse link) from the starter relay. The yellow/white wire (connects through a brown fuse link) connects through the green fuse link and is needed for proper regulator control. By removing the black/orange wire, you have disconnected the yellow/white wire from the battery.
Q3: Do I just follow the other two back until I find where they split, cut it, and splice in my 4 AWG wire?
A3: No. Run the new 4AWG wire from the stud on the back of the new 3G, through the new fuse, and then to the battery. Leave the old Black/Orange wires alone and definitely don't remove anything from the starter relay end.
Q6: It's about the two wires that were left over from the square connector. Do I just cut and tape them off, or do I need to run them to the stud on the alt. too?
A6: You could do it either way. I just left the big square connector on, plugged into nothing. If I ever wanted to put a 2G in (don't know why), I could.
Q7: What I mean is, do these wires serve any purpose now?
A7: They serve an important purpose by being connected at the other end (at the starter relay). The statement "...you can either take the 2-1 10gauge wire out or just tape both ends and get it out of the way..." is incorrect. Your regulator won't work properly if you disconnect the 10AWG wire at the starter relay. If you do remove the 10AWG wire at the starter relay, you have also inadvertently removed the Yellow/White wire from the starter relay. This wire comes from the d-plug and is required for the regulator is work properly.
Read the 1st few paragraphs of the link I gave you. The explanation is right up front about why this is all necessary & why the Ford design was so poor. This isn't the only circuit with a poor design. The headlamp/fog lamp is another one.
I have that write-up on StangNet.
https://www.stangnet.com/mustang-forums/resources/87-93-gt-fog-lamp-main-light-switch-fix.59/