You won't be able to install CIA's launching ninjhax in emunand because rxtools/pasta loads a firmware that doesn't support the required exploits. Someone correct me if I'm wrong. I have been working on the same goal for a few hours now. So far what I have found is that the only working method of installing a working FBI into emunand on a N3DS is by injecting it over an existing app, usually the Health & Safety app. This is exactly what I have done with help of decrypt9 and universal inject generator.
However I face a new problem. I can launch the latest FBI just fine in emunand now but it will always hang when attempting to install a CIA. No errors this time just stuck on the progress bar screen with 'Press B to cancel'.