First off thanks for the guide; while I wasn't able to successfully do everything it served as a nice starting point for further research.
Here's some feedback on individual steps: (I used an old 3DS with sys menu 9.2)
1.3: I could never get HBL to load again through browserhax after I used the Pasta Patcher. So, I went ahead and installed themehax, which defaults to load HBL on startup. This actually made things easier for me than fumble with browserhax, as I found the boot rate to be rather poor.
2.1: I could never get ninjahax to work. I installed the game, went into the QR code scanner, scanned the code, and the game just froze. Every single time. I even searched for the JPN version and used the JPN QR code, but no luck there either. I finally followed a chinese guide that had a QR code to
http://go.gateway-3ds.com and that successfully booted the Gateway menu. Everything worked, too (both NAND backup and emuNAND formatting). As such, I don't think cubic ninja is necessary at all.
3.1.2: your rxtools folder is set up incorrectly for old 3DS unfortunately. The 0004013820000002orig.bin is for new 3DSs only; for old 3DSs it should be the 3485 KB version straight from Nintendo's servers IMO. BTW, this file needs to be named firmware.bin and placed in rxtools/sys for old 3DS.
3.1.6: "DontTouchThisYet1" should be changed to "CBM".
3.2.3: No idea what this should be, but "DontTouchThisYet2" doesn't exist.
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Yeah I'm on N3DS. 9.0.0-20E
I've tried everything too. Looking for details in every guide I can find. Emunand just will not load.
The error message "Failed to load Native_Firm: 4" means that the firmware.bin file (or in n3ds case 0004013820000002orig.bin) is corrupt or missing. For me once I put the correct firmware.bin file in place it worked, but obviously this will be different for new 3DS. Sorry can't be of much help :/