what is my system's weakest link?

Those Thiels would benefit from, and you would know it immediately, an amp supplying them with a stouter power supply.

the room, which it is for all systems.

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.