Hi,
I am facing also speed issues on my iMac. Although my copy is running stable, inserting and formatting the citations take quite a long time even on my very fast iMac. From my experience it looks like EndNote has some general “speed issues” regardless of the size of the document one is working with. Comparing to the “Papers” software for the mac, EndNote is far slower handling my 600+ papers collection. But in your case there might be caching or swapping issues on a slow hard drive (?) or due not having enough RAM?