Download issue confirmed, and should be fixed now.
Post bug reports in the IMS thread please, I'm going to loose oversight real quick if I have to handle them in different places. There were some strange things with RC3, please see if RC4 fixes the issue. If not, feel free to post the scenario in the IMS thread.
IMS only works with individual modules, it cannot apply its functionality to an already existing vessel. You'll have to build your station/ship from the modules provided with the download.