yes, that's exactly what I've done.
I've had 2 versions of virgin NAND, firstly I got just 4.2E and IOS70, that went through setup and wouldn't boot a second time.
Then I stripped down my NAND dump, deleted all but EULA and Region Select, installed latest versions of every IOS (excluding stubbed and old System Menu IOSs), ran that and it worked straight away (no setup).
I then DLd the last 2 I hadn't replaced and made an entirely new NAND from nothing, copied the settings.txt and ran that. It worked, I got through setup, tried to boot it again... nothing.
I'm now manually comparing my dump and virgin NANDs to see what the file differences are (not under hex, just file sizes and existence) to see if I can find any important seeming files missing from the Virgin one.
Just trying to filter out all the save games, they seem to be in title/00010000-00010004 except 00010002, which is empty (makes sense as they're missing from my virgin NAND, and the filesizes decreased when I deleted save games). However, when I delete the all 4 directories it wont boot, yet when I copy them back it boots and recognizes all the ones I had previously deleted in Wii settings. Confusing. I really wish there was documentation for all this.
UPDATE: Get this, I used format system memory on my working NAND dump, and when it was done, I set it up just like my virgin NAND, then when I rebooted...IT DIDN'T WORK! So obviously whatever makes this work is deleted when the Wii formats itself. When I looked at the save game folders, they still had folders inside them so I will check so see if any files still exist, and if they all do (maybe the Wii just deletes indexes rather than actually formatting) I should be able to find missing files... MAYBE...
Update 2: I just manually deleted all my game saves (took AGES), looked at the NAND and all the folders are left there empty, but some still have TMDs in them. I filtered out the folders with TMDs and deleted the remaining empty folders, and that wont even boot. I've also tried deleting tmds.sys, but it got recreated as 0 KB and it didn't boot.
Update 3: Last of this post as I'm out of ideas... I reset the NAND to just after I had finished deleting saves and guess what? IT DOESN'T BOOT... so there's no point in continuing with this NAND as it obviously doesn't function.
Up side is I now know deleting all my saves stops it working. I wondered if a 0 size tmds.sys was causing this (because on saves and no channels should equal a 0 size tmds.sys) but if I remember correctly it was still 54KB (presumably because of the remaining tmds, likely for channels on SD), however lack of channels or saves may be an issue as Wii normally has Mii, Photo and Shop...
First I tried making a game save, I put in a disc (crossbow training), forces wii update, attempts to restart and doesn't...
Started over and I tried adding the mii channel into the mix and it appeared, I loaded it, made a mii, all seemed to save fine... went back to wii menu using HOME, didn't load...
Tomorrow I may try Red Steel instead (this might not force an update) to make a save, and maybe a VC/WW wad instead of Mii channel to make a Channel AND a save.
When I wake up I'd really like to see some fresh ideas from you guys, i'm not really getting anywhere.... (and don't suggest giving up, that doesn't help... there must be a solution for this, people are using it fine)