Here are my results, after some fooling around. There may be more info than necessary here, but I figure that's better than too little.
4.0U, rev14, bootmii, preloader, and custom theme installed.
First, I made a NAND dump with FS Dumper, transferred it to 8GB Sandisk USB stick. Here's where I'll ask you to please not flame, I did something foolish just for the sake of foolishness... i erased the entire contents of the title folder to see how far I could get (I'll admit I've never seen a NAND dump before, and knew I'd be erasing something I'd need, but anyway...)
Installed Eduardo the Samurai Toaster and Swords & Soldiers (both ntsc-u) with Wad Manager 1.5 to the USB NAND. Both installed fine, Wad Manager expectedly froze on "Restarting Wii", powered down and started up again.
Loaded Triiforce, loaded USB NAND, both titles showed up fine. Tried to start S&S, froze on first logo (surprise!). Tried ETST, loaded fine, said yes to create save file, continued. After trying to load first stage of the game, got an error that Wii System Memory couldn't be accessed (surprise #2).
Made another NAND dump after erasing all VC/WW from SD Card menu, and moving 3 forwarder channels back to Wii Memory, left teh dump as is, tried installing same 2 titles. Got an error -1024 on the second game, tried uninstalling and reinstalling, another error. Exited, power down, etc, came back into Wad Manager, installed second title, success.
Loaded Triiforce again, USB NAND, only get ??? where titles had previously shown up. Tried scrolling through titles, only get ???. When trying to start, get the error about main.dol not being found, press A to load nand loader instead...
Code:
Loading DOL: /title/00010001/43554245/content/0000001.app
ISFS_Open /title/00010001/43554245/content/0000001.app failed -106
Reading .dol failed
.dol loading failed
press any button to continue
Changed Video Mode to NTSC480i, get to "Loading complete, booting...", then code dump. Changing any other settings gets me the .dol error again.
So, I feel as if I'm trying to load titles which aren't the WiiWare I installed, but instead the channels that were on the emulated NAND. I also wonder if having a custom theme installed would change things. Going to try to uninstall all installed channels that were on original NAND, and report back later.
Sorry if I'm just doing something stupid, just trying to post as much info as I can in case there's something that catches your guys eyes. Thanks for this, I know I will get it working, and I couldn't appreciate your guys' work any more than I do. Cheers.
Edit: I deleted the contents of /title/00010001/, as BlackVivi had reported success with doing this. Installed same two titles again, now only those titles show up in Triiforce's list. Loaded Eduardo Samuarai Toaster, once again got "could not access Wii System Memory" after trying to load stage 1. Tried loading Swords & Soldiers, get to wrist strap screen... this time, wiimote loses functionality and won't sync. Powered down, Wiimote now also fails to sync on normal Wii Health & Safety warning screen, but will sync once the system menu is loaded.