I did do the big 3 with 0 guage a few days after I installed the subs, but if anything it made the headlight problem worse. The battery was an autocraft gold less then 8 months old. I'm guessing the alternator wasn't able to provide enough power so it kept trying to pull from the battery which killed it.
The amp is grounded to the rear strut tower with 4guage (same as the + wire) and definitely has good contact. I dont know a ton about car electrical, but im not sure what else the problem could be aside from lack of power from the alternator. It is 16 years old so its entirely possible its just not putting out what it did back in its early years.