I've had no problems using either the straight or flared interstages when building Thor or Atlas crafts. Note that both interstages connect to the engine mount rather than to the bottom of the A or B/D tanks so you need to remember to include that.
All the parts that you list are from non-KOSMOS mods, namely KSO, HullCam and the ISS Community Project (and probably Lazor's Robot Arm), not sure what this would have to do with KOSMOS? Are you trying to load a specific craft file from some mod?