First: Did you try a version 3 webos quick install? I think I'd start with that...
Then I would solve the root certificate issue:
1. Go into Software Manager, Tap on HP App Cataloge, tell it to not download the update again.
2. Start up the HP App Cataloge. If that only gets you to Software Manager, you did something wrong in 1.
3. Search for "App Catalog Update" and install that. It will work if installed from the App Cataloge.
That's it. You're done.
To be sure that no background installs are going on, I'd now look into software manager again and tell it to do all it's updates (including the App Cataloge one you canceled earlier) and wait for them to finish.
Do you know a good way for you to get a command line for the device? I think the easiest might be Quick Install... best would be novaterm. But that's only in the SDK and on Linux (might be Mac also). You could also install the OpenSSH Server and use that if you have a private WiFi at home and are comfortable with ssh-keys....
Anyway, it would be good if you could do a "df -h | grep db" on both of your devices and can somehow copy the results and compare them (or post them here). I should have come up with that earlier...
On my Veer (with webOS 2.2.4) the media db partition has a size of 135MB... it's the first number that you'll see. The most important part would be to see if the numbers differ on your both devices. If that is not the case, then we were on the wrong track... :-(
If that is the case you can follow this guide to resize the new one to the same size of the old one and try restore again:
MojoDB Partition Resize - WebOS Internals
BTW: To trigger restore, you don't need to doctor. You can just use the device info app, in the reset options select the first red option, something like "delete apps and data" (My system is set to german, so I translated them back to english, your button descriptions might differ slightly. ).