Manually editing your registry settings should be done with extreme care and not before taking a backup. In most cases, I wouldn't recommend editing the registry unless you are absolutely positive there will be no negative downstream effects.
When you tried unregistering with the ESRIRegAsm.exe application, was it a 10.0 or a 10.2 ESRIRegAsm.exe executable? If the registration was initially performed with a 10.0 executable, then perhaps the unregistration process must be performed with the same version. That is the reason I asked earlier if you had upgraded your desktop software from 10.0 to 10.2 yet.
EDIT: Can you try this real quick? regasm c:\WatershedSOE.Manager.dll /u
The regasm.file can be found under the .NET framework directories; for example: C:\Windows\Microsoft.NET\Framework\v4.0.30319. Try the command above using the regasm.exe under a 4.0 and a 2.0 .NET folder.