Chris,
I have had your problem. Not to sound mean, but I would sell your system and start from scratch. In my younger years when I ran a high end store, all the Manufacturers woud run contests. I acually won an Adcom stack, (GFA-535, GFP-565,and a GCD-575) I was using a pair of Kefs back then and could never get the system to sound right. It was the earlier Adcom stuff's sonic signature which just make my ears bleed on any less than perfect recording.
I actually sold the pre-amp first then picked up a CJ PV-10A.. Wow! Things sounded a heck of a lot better. I then picked up a Sonographe (Lower end CJ amp) and things fell into place. What I would recommend you do is sell your passive controller, your amp, and your cd player and purchase a nice integrated amp and modern day CD player such as the Creek or even NAD depending on your budget. You can get some real deals on mint used gear here on AG.
Just my advice based on my experience, not trying to add insult to injury.
Good Luck!
Chris