Upgrading Entire System...please help

I think you can do extremely well for 6 K especially second hand. I would not worry about CD or Amplifier except to get the features you want and at a good bargain price (second hand - so just keep an eye out - use audiogon bluebook). Speakers have a much greater impact - I would choose these carefully for 3 K second hand you can get some great quality speakers, if you are prepared to be patient and don't mind too much about aesthetics (black ash instead of expensive fine quality wood veneers).

If you are worried about amplifier matching then try to get active speakers...these are well known to sound slightly better than their passive equivalent, are common in pro use and are gaining acceptance slowly in comsumer circles.

You could call audio stores and ask them to put together a system in your price range(assuming you have all the money now) and see how you like it. I would not make a decision right away after the audition. I have been upgrading my system recently, and I started at the front end. The advantage and enjoyment of doing it this way is that as you improve your front end, you improve your speakers at the same time. I'm getting close to speaker replacement, and I'm thinking that I would have to be able to try them at home. Some of my upgrading was out of need. I blew an amp, lost connectors on another amp, hum developed on my preamp, speaker cables blew up two other amps, some interconnects shorted out, and I lacked a proper cd player. I started by getting a conservative choice of turntable(circa 1992 fully kitted Linn Sondek with Mana Sound Table) then an amp to replace a blown amp, then cables that didn't blow my amps or short out(getting advice from Plato about what cables work well with my amps). I didn't believe in cd, but Alex of APL Hi-Fi proved to me that cd can be a viable source, so I got one of his players. I used various isolation devices. When my preamp developed a hum, I brought one home to audition in my system and bought it. I believe the Rega is the choice at the price range you mention. I had it much harder, as I had trouble handling cd, and my cd player was designed with analog in mind, and compared to analog(Alex has a DAC, which could be combined with a cheap transport). Of the amps that you mention, the newest Naim Nait has had favorable mentions, but might limit your speaker choices due to power limitations. And it is expensive. My speaker budget limits my choices(maybe Revel, or Dali-both liked by the audio press). Don't forget wires, tweaks, and room acoustics. Cheap wires like Speltz anti-cables have had good press. I personally like Oritek X-2 interconnects a lot(He makes a DAC also.). Cheap power cords would include Volex 17604. Cheap isolation might be myrtle blocks with isonodes(BSA) under them. There are cheap racks(Adona,?),cheap room acoustic treatments, cheap speaker stands or supports(spikes?). I was really blown away by the difference dedicated lines made to my system. Here on Audiogon, JsaWhitlock, does dedicated lines. I'm sure that expensive system you heard has dedicated lines. Part of the enjoyment that I get from upgrading has to do with changing one thing and seeing the effect that it had on my system. But there is an advantage of the whole system done by the dealer approach-no expensive mistakes!

I want to add an addendum to the above. To get an idea of class D amps, add the Nuforce Ia-7(with V-2 boards) to the audition list. Naim should be used with their own power cords and interconnects, I believe. Separate power cords from signal cords. You can try lifting signal cords(and maybe power cords)up from the floor(I used styrofoam cups from the Dollar Tree-not the best, but cheap to try.). The reason I mention these cheap tweeks is two-fold. One, many can be done now, and prevent you from spending money quickly and allowing more money for amps, etc. Two, you will need to do these kind of things anyhow to get closer to how your friend's system sounds.