Hi John,
Have you posed this question at other forums? I'm sure there are other forums out there that will give you completely different opinions on this subject.
First, let me state that I'm not into tubes at all. I don't have them in my system now, though I used to have a tube in a Cal Audio Labs DAC. I do use them in guitar amps, but that's totally different.
So, without being an expert, I would imagine that there are tube amps out there that will suit ones needs based on their speakers and listening habits. I don't think that it's necessary to clip a tube amp, if it's played within its limits. The other technical arguments against tubes? I'm not sure if they matter or not -- it would take a lot of time, reading and research to fully understand everything that's been said thus far.
Regarding having a "transparent" and "neutral" system without any coloration whatsoever -- I'm not sure how much that matters, either! A better goal for which to strive might be a system whose sound you enjoy. I believe all systems will have some coloration to them, especially due to speakers, and there are many ways to enjoy music playback. There are so many measurements, tests and rules for all this... it definitely takes some of the fun out of it for me. I've been reading some photography sites, and one guy suggests that it's not important to create a perfect representation of what you've seen, but rather an piece of art of your own. Although somewhat different, the same goes (IMHO) for an audio system. It's an experience in putting pieces together. Otherwise, if we go on suggestions here, we'd all end up with something like this OnkyoReceiver->MonopriceCables->BehringerEP2500 because it'll measure perfectly and is the biggest bang for the buck. Well, maybe that's true and maybe it's not, but it doesn't make for much fun in this hobby.
So just go out and listen to tube and solid state products at your local dealers. Listen to the cheapest tube amps and the most expensive and see what differences you find. Same with tube vs. solid state.
And, yeah, there are lots of pieces out there that will get you in under $5k for preamp and amp.
Good luck!