Nev, I went ahead moved the cache up as suggested and that helped tremendously! I had also put a ticket into our Microsoft partner and heard back from her shortly after I made the adjustment and she confirmed this is the first thing they look at when speed issues are present. She also suggested that with the native database I split the database up into 3 or 4 separate files rather than just using a single larger file. Our database is currently 6GB, she suggested using four 2GB database files instead. I haven't tried this yet as we seem to be running much better now so I'd rather leave well enough alone for now.
Thank you for your help!