Well, it seems to work on both my US and Australian N3DS. As I mentioned on the plugin's thread your save manager does seem to have solved the problem of 6.x key save conversions. Still, as happy as I am to have that one save converted, the only other thing I could think of to test was the multi-region. So I tried my US Sky card on the Australian model, and, frankly, EU functionality isn't looking so good. I got several black screens, lockups, and "card has been removed" errors. It even gave me that last one on a game from it's own region. Running EU games on the US unit went much more smoothly on the other hand.
One thing I noticed. A pre-existing Gateway save on the copy of CN can mess things up. I know, I said I was going to overwrite Ninjhax. Well, for whatever reason (maybe I was sleep deprived), I had placed it first on the cart. So, I decided while I was at it to move the Gateway saves up to Ninjhax's position. This caused many problems initially. Since my primary focus initially was to test the save plugin functionality, I decided to dump CN's save (besides, it's crossed my mind to have a look at your payload with a hex editor sometime). Surprisingly, the Gateway payload was still present. So I loaded my Ninjhax saves to the copies I was planning to use for NTR and redid the QR code. Then it started working alright.
So, it works.
Now, I hate to make another request so soon, but there is one thing that keeps me lugging my old 3DS around. And with your CFW running from SysNAND, it's in the perfect position to solve it. DSiWare. I know, you're "anti-piracy" but, with the DS being previous generation, and no longer on store shelves, I thought you might make an exception. Well, only one way to find out. Ask. And no, I don't expect you to pull a 180 on your "no CIA" position. I can use Gateway Mode to install the DSiWare. All I'm asking you to do is enable the execution of unsigned DS code, so I can run "Zelda: Four Swords" on my N3DS. It should be possible to do this while leaving the other checks intact. Besides, it will give me a reason to continue testing your releases (though it's probably not like you're hurting for testers). Since SDF and DSiWare are the only things I've ever used CFW for, as far as I'm concerned, that's the only thing it's missing at this point. Add it, and we can declare the old 4.5 CFW dead at last. And I can leave my old 3DS at home, and only use it to decrypt free eShop content (since it doesn't look like they're going to be able to keep EmuNAND current on the N3DS, we'll always need the old one for game updates).
I still think it would be interesting to see a CFW give the Sky3DS all the capabilities of the Gateway (especially with the Gateway needing a swap now), but I can see that's not where this train is going. The inability to install anything really hurts its flexibility. It's like having the Wii "Homebrew Channel" without the "WAD Manager", a PS3 CFW without a package installer, or a PC that boots from a DVD drive and has neither hard drives nor USB ports. Sure, you've prevented so-called piracy (and therefore reduced sales). Because you've effectively made sure that NOTHING WHATSOEVER CAN BE INSTALLED. Sure, no one can install a downloaded "Majora's Mask" CIA. But no one can install PRBoom or BlargSNES either. You can't even install a game update (and now that 9.6 is out, it's probably much too late to add EmuNAND functionality so that updates can be grabbed from the eShop). If you're really that concerned about misuse, just have the CFW shut the N3DS off upon launch. Then there's absolutely no way anyone can misuse your CFW