Finally got the SQL 2000s wired up and broke them in this weekend

I ran a similar setup in my Silverado for a couple years and learned the second battery thing the hard way. Threw one in the back thinking it would fix my dimming, and it did almost nothing, because the stock alternator was the real bottleneck. The battery just sits there as a buffer, and if the alternator can't keep up with the draw on the big bass hits, you end up with two half charged batteries instead of one. What actually helped me was doing the big three with some 1/0 cable I had left over from the amp wiring, and then eventually a ho alternator once I could afford it. After that the lights stopped dipping completely. So if you add the second battery and it only mostly settles it, the wiring upgrade is probably going to do more for you than you expect. Also on the break in, I did mine with actual music at low volume for a couple weeks instead of sweeps, and the suspension loosened up nicely either way.

Funny reading this because I skipped the break-in period entirely on mine. Installed them on a Friday, turned the gain down to half, and just let my daily driving do the work over the first week or two. Never measured a thing before and after, and they've been going strong for over a year now with no issues. Maybe I got lucky, but I think people overthink it a bit.

On the electrical side, I'll say the big three upgrade was the single best hour I spent on my whole build. My grounds were all factory and honestly kind of crusty, and just cleaning them up and running proper gauge wire from the alternator to the frame and battery cleared up most of my dimming before I spent a dime on anything else. I also went the opposite direction on box tuning than you did. I wanted more of a punchy sound for rock and threw together a smaller sealed enclosure instead of the ported one I had planned. diferent goals I guess, but it's interesting how much these respond to what you put them in.

Ha, this brings me back. We used to tune boxes with a test tone disc and a multimeter back in the day, none of this software modeling stuff. Half the time the 'designer' boxes we bought sounded worse than a well braced slab of MDF with a properly sized slot port. Your comment about them sounding looser after a few weeks tracks with every set I've run too. Curious what volume you ended up at and where you tuned it, those two numbers make or break these subs.

Gotta disagree with the Silverado guy on the second battery being useless. Mine cut the dimming way down, and I think it's because of where it sits. The amp is pulling thru a two foot run to the battery in the hatch instead of sixteen feet of factory wire from the front. On a hard hit that short, fat connection delivers current the stock charging system never sees through the long run. Is the alternator still the weak link in the long run? Sure, but the battery covers the transients. Sounds like the OP is in the same spot, battery helped but didn't finish the job, wich tracks with a stock charging setup that's just undersized for the demand.