Where do I go from here??

I've been reasonably satisfied with my current system, but I'm looking for more. What is the best upgrade I can do for $500-1000?

YBA CD-3a -> JPS Superconductor+ -> Integre DT -> Bi-Oval 12's -> Silverline Sonatina mk1's. Power cords are some Stealth Audio's I picked up for pretty cheap.

The YBA has a rather lean tonal balance, and I'm growing a little tired of it and want something more seductive. What I really miss is the presence and 3-dimensional soundstage that I commonly hear in tubes, so I'm inclined to replace the Integre with a tube amp. My only concern is that I will have to sacrifice dynamics and detail?

Another option is upgrading my cables, getting a good rack (components currently sit atop BDR Cones on a sturdy but non-audiophile table) or adding some power conditioning, but in my experience these things only improve the sound in subtle ways and do little to actually transform the character of the sound. Is there anything out there that can make a substantial difference?

I have the same speakers and use a Pass Labs Aleph 3 with a Pass labs Aleph P .... the combo sounds great!!
Try flipping your BDR cones over, removing them or moving them around underneath key components inside. I found that the #4's detailed/leaned out my system, and #3 were much more neutral. Vibrapods helped or just plain sorbothane underneath your CD player might help.
You could try a tri-phazer. With a 90 day money back guarantee you have nothing to loose but distortion..

Have you considered upgrading your CD 3 to a CD 2.....huge difference! The soundstage is bigger and the bass is better. Probably the best $1000 you can spend without starting over. Good luck. You have the foundation of a great system!