When I did the big 3, I went power from alt to battery, then upgraded the battery ground, and also the engine block ground, left all the stock wiring for the charging system in tact.
No problems at all, even with the 145amp alt

 

What is the Big Three

 

Explained in this thread already.

But to simplify it, its upgrading the "big 3" power wires to a larger gauge of wire.

Alt power wire to battery
Battery ground to chassis

and engine block ground to chassis.

 

Hate to dig up an old thread.. but I am in the process of doing the big three right now and there was in fact a fusible link in the original wiring. It has a 10 on which by my understanding makes it a 10 guage link. it connects to the mega fuse under the battery on the same side as battery+ .The other side of that fuse connects the underhood fusebox and airbag sensor.For wiring I used the original body, frame and block grounds. Then added a secondary 4 guage from batt- to frame and alt mount bolt to frame. Positive is all original except for a 4 guage from battery positive to alt stud. Unfused