O wow, hell ladies and gents sorry I hadn't replied to this post. I picked up my nexus a couple days after launch and at the time this thread had died down and I just plain forgot about it, I do apologize. Unfortunately there's a crap load of posts to catch up on and I haven't slept since weds so I'll try to hit as much as I can and will finish tomorrow.
First I'll finish my little disclaimer by pointing out it might be a bit rusty as i haven't worked on the x in quite sometime save for helping a buddy out (bmc shout out). For the same reason I'll start by answering one of the last questions, seeing as how I have a nexus and can't use the same excuse lmao.
The gnex uses a very different system for its wifi's software/firmware. There isn't too great a need to do the manual calibration via basically, at least in my mind, a glorified .config file. All those numbers and letters and spaces and whatnot all signify a configuration setting for the phones wifi, everything from interface, mode, power, and throughput, right down to what flavor fail flakes it chooses to have that morning. This is why you will see differences in said configuration values, different phones call for/can handle different things. The coding itself is fairly ubiquitous amongst a large number of phones due to the prevalence of TI and that chip as well as the omap boards. As a matter of fact the reason that second post I reserved was never filled is because you can actually force the hardware to believe its full-out top-of-line N and "activate" a whole slew of mods such as burst mode, etc. Only problem is .... while it thinks it is and says it is .... it really ain't lol, its merely mimicking in title alone what other phones can actually do. The gnex however has a much more robust and easy to use configuration method (and source code lol), hence the lack (more or less) of crazy strings of digits. Also it uses a different file configuration then the X and the nv is created/stored/used/ etc differently.
Another quark of the wifi system is responsible for another issue somebody had, if I had to take a blind guess that is, as it was the culprit many times over in the past. One of the most fickle and annoying problems a lot of android phones used to have (some still do) is the wpa_supplicant.conf file. Normally this file is pretty harmless, which is good considering it stores information that makes the wifi all happy and stuff, in this case though it could easily turn into a pain in the ass. This is because normally if the file gets updated with new info it just takes it or if needed remakes itself ... the X's however doesn't always act like that. Instead its supplicant file erases itself entirely if you tamper with it at all, hell even when the system does it it still will erase itself or become empty/blank. When this happens your wifi is unable to really function as it doesn't have its info and it makes it go bat shit until its properly remade by the system. One thing you could maybe try the next time it goes wonky on you (assuming you have a backup and/or replacement on your SD or somewhere) is to make it write able much the same as you would edit a grub.cfg file in linux. In a terminal try:
chmod +w /path/to/wpa_supplicant.conf
Then either fill the info back in or repeat the commands except make the replacement write able as well before you replace em. Once your done with either choice and everything's gravy just undo the command:
chmod -w /path/to/wpa_supplicant.conf
Careful tho, while it works just fine for grub I havent tried it myself on the pita supplicant.conf of the x.
As to the discrepancy of where the nv files are supposed to go, you are correct in that it usually goes where it needs to on its own. However, for whatever reason, it doesn't always go there so (for me it had appeared in /data like it should have but also had appeared in / and /system too). I added that line to cover all the bases and so folks didn't freak out if it showed up somewhere else, guess that game plan backfired lol...
Another line that was asked about was the init edit. All of those init scripts come from the boot.img and are created every boot, which is why even after editing them they go back. As to why root explorer didn't work for you I'm not sure, I'm going to guess it was an issue with permissions. You can also proc the script via the emulator or try not editing the script as well.
Again I apologize for not seeing this in so long and should prolly apologize for the rambling wall of text too lol, sleep deprivation is a bitch haha. I will try to get back and finish answering questions and helping those that still need it out. For future reference tho please feel free to pm me if I don't respond here as I normally don't read thru these boards anymore.
Edit: mig pm me a log of your gnex. I haven't heard of this issue on our nexus. I more or less use aokp in a way too and haven't had an issue, so I'd be interested to see what's up.