With regard to the input signal, I was thinking in terms of the headunit volume...if the 360 has a separate volume knob, you should have your head unit or whatever other source at approximately 85% of full volume before you even start fiddling with pots on the 360. I would imagine the instructions say something like "set head unit volume to x, then turn pot on 360 'til clipping light hits, then back off"? You can go slightly higher on your head unit volume, if you don't quite push the 360 enough to clip it, but it shouldn't be a real concern if you don't...provided your signal chain is relatively noise-free.
With regard to ground, I hope it isn't "bare paint", but "bare metal" under that "large bolt/lug" not "screw".

That DC power supply sounds like a problem...rest assured, if it operates, it's grounding itself somehow...which is scary if it powers up at ~45 watts or so and no connection to vehicle chassis ground...that means that it and everything powered by it is floating, or grounding itself via some goofy means like from the computer case to the carpet in the trunk (not good)...difference in sound between ground connected/not connected? If your PC/PS is grounded correctly, it doesn't mean that other paths to ground don't exist, it just means that your proper path to ground looks a whole lot better to Mr. Electron.
I imagine you have a low pass filter on the amp powering that sub, right? You should be fine with that, I would imagine. The TA on the .2 is where you're going to see the benefit...am I correct in that the .1 doesn't have time alignment? To me, that alone is worth the upgrade.
Spring is coming...i tell you what, if you end up with the .2 (or either way, really), I can help you get it set up at a meet or something...oh, and we gotta compare baby pictures (I got a new daughter since last we spoke

).
That Acura of mine...far from perfect, imho. I did, however, find a number of things wrong with my setup since last we spoke (gains, sound card output), as well as upgrading the sub to a single 10w6v2...the system is sounding much better, and should be ready for a thorough demo by our spring meets.