What is a good efficient way to isolate clips from long movies?
What format is your long video? The seeking performance problem may not be in Kdenlive but in your movie. If you aren't yet, you should consider using a container format that has index tables.

Now regarding extracting a clip from a movie, I believe you can do that with ffmpeg, specifying a codec named "copy" and setting a start position and a duration (in seconds):

ffmpeg -ss &lt;start-position&gt; -i &lt;source-filename&gt; -vcodec copy -acodec copy -t &lt;duration&gt; &lt;destination-filename&gt;