what is my system's weakest link?

I have a different take on this. The "weakest link" is the Project tt. The biggest "problem" is the Thiel/Brio combo. The Brio is a nice integrated and while you mention wanting a new pre, what will you do about a power amp? The C28 is a good vintage pre, but do you really want to open up that can of worms (restoration/reliability of pre, new power amp)? If it were me and the goal were the best possible sound for +$1000 or so, I would build a new system around the Brio which is a solid integrated, get friendlier speakers (I like the Vandersteen suggestion) which you should be able to buy with what you get for the sale of the Thiels plus a little more, and GET A BETTER FRONT END; something like this (no affiliation):

http://app.audiogon.com/listings/turntables-vpi-traveler-v1-2013-11-06-analog-90039

or even better:

http://app.audiogon.com/listings/turntables-exquisite-well-tempered-lab-record-player-optional-dust-cover-with-marigo-audio-lab-p-2013-11-02-analog-94925-corte-madera-ca

I think you will have infinitely more satisfying sound this way. Good luck.

Music Direct has some great process on Focal Chorus 800 series speakers. I have never heard a Focal speaker that I didn't like. The 816v is a fantastic choice in my opinion.

Bottom line is how much do you like the THiels and want to invest in getting the most out of them. AN amp upgrade would be the initial solution.

Focal is a good option to consider. They are much easier to drive than Thiel in most cases, and I tend to think of the two as being in the same general sound quality camp when things are going well. Worth considering. Triangle (also French like Focal and also generally much easier to drive than Thiel as well) would be another.

I see that the consensus seems to be that the speakers should be the first to go, I have to say that they would be my least preferred component to switch out, mainly because they fit beautifully in my space, which might not be able to accommodate every speaker, and though its superficial I really like the way they look, I have to say that the exterior of gear is quite important to me (and to my wife :)..) + speakers are hassle to have shipped to you etc.. oh and I think the sound great I mean I never thought they would be the main reason why my system isnt all it could be..

I guess thats why I felt prone to getting a new pre and power.. instead of the brio or perhaps getting a new cartridge for the TT or a new table altogether.. very confusing times.. hard to figure out what sould go :)..

During my crazy days of changing equipment almost as regularly as my underwear I owned a pair of Thiel 1.6s. They were only a little larger than the 1.5s but they were so much better to my ear. Much smoother sound with deeper bass. Also much better looking IMO. You can find them for less than $1k used if you watch.
I still prefer the sound of the Vandersteen 1c in that size and price.
All of my searching was an attempt to better the sound of my old Meadowlark Audio Kestrels. My quest seemed to focus on time coherent speakers such as Thiels and Vandersteen. There are a lot of nice options out there but I gave up searching a couple years ago.