Sorry for the delay, it's been a busy several days and I didn't get any notifications there was replies, so I completely missed these posts until now!
Have you used any C# scripts in your project, without necessarily Twisted IK 2 enabled? It seems like it might be something with compiling C# scripts that is causing the issue, at least I think that may be the issue. Can you make a new project, add a C# script, and then see if it builds and runs successfully? The script doesn't need to have anything in it, I don't think, but it may help narrow down if the C# build process itself is causing the issue or if it's something else.
Also, are all the issues mentioning "Cannot instance script because the project assembly is not loaded"? Does the top issue mention anything else, as it could be that one of the issues is causing all the others.
Sorry again for the delay in reply and for the incontinence!