Diagnose the weak link.

I'm enjoying my Sony XA-5400ES CD player mated to my new Bryston 4B SST2 power amplifier & Thiel CS 3.6 loudspeakers. My preamplifier is a 25 year old NAD (#1130 I believe?). The sound is powerful with bass that needs tidying up. I plan to put the Thiels on Sound Anchors stands to try to focus the bass. Where I need help is with trying to separate out the layers of sound during loud, complex passages. Also vocals seem recessed and lyrics are hard to make out. The sound from this system is getting better (compared with my old system) but I really need some guidance to separate out the layers of sound and achieve the higher articulation this system should be capable of.
The NAD is definitely the weak link, IMHO. There's a VTL 2.5 line stage on e-bay right now that ends tomorrow (Friday) at 7:00 EST that I think would suit you. I once ran the Thiel 3.6's with a Levinson 27 amp and the VTL 2.5 pre and the Thiels sang pretty nicely.
I agree with Ncarv; time to upgrade your preamp. You might also consider a CJ pre.
Yeah, I kink of knew it must be the preamp but wasn't sure how significant the preamp was on the total sound. Right now, many rock CD's are just way oversaturated and only the quiet passages are listenable. I really like Smashing Pumpkins but the CD of there's that I got from the library was so distorted and tinny as to be unlistenable. The same for many, many CD's. I'll look into the VTL 2.5 on ebay, thanks, (& Conrad Johnson too - although I wish I could find a CJ in black that would match the look of the Bryston 4B. What is folks opinion of the Bryston BP 26 by the way?
Nada Nad
Certainly the NAD pre is suspect, but your complaints make me consider whether or not the room and/or placement might not be a bigger issue.
I have a very similar set up: Sony 5400, Thiel 3.6s, Parasound Halo A-21. I recently borrowed a used Audio Research SP-17 line stage from a dealer and was very happy with the improved dynamics and cleaner bottom end (nice phono stage, too). Unfortunately, I couldn't work out a good price on the preamp, but I did find a nice deal on an SP-16, which will be here next week. Like others have suggested, I believe that adding a high quality tubed preamp is going to help a lot with your Thiel/Bryston combo.

A couple of additional thoughts from my own experience. The Thiels have a very strong mid-bass that can easily get out of control if your room isn't ideal. Placing the speakers along the long wall of my room really helped clean up the bottom end.

Also, don't expect much forgiveness from your current set up on badly recorded, over-compressed rock albums...even with a better preamp. Good luck.
"although I wish I could find a CJ in black that would match the look of the Bryston 4B"

Black and gold is a nice color combination, IMO.
Glad youÂ’re losing the NAD.
If your system only consist of the CD player, speakers, amp and pre-amp and if your CD player has an internal volume control, then take the pre-amp out of the circuit altogether and run the CD player analog output directly to the amp. If you want a pre-amp because you have other sources, then a different pre-amp may be the way to go. Also, I can guarantee that your analog output from the CD player is not up to snuff and a DAC will dramatically improve your CD player/transports sound.

For most CD players, the internal DAC is a weak link 1) because they are not typically as good as the digital circuitry in a stand alone DAC and 2) the power supplies are inadequate for the analog output stage.

I'm not sure if your Sony ES unit has a volume control, but if it does, nix the pre-amp if that is your only source.

I would consider a Modwright 9.0 pre. My 4bst works nice with mine.