I was unable to use the 25c Continental Grand Prix 4000s tires on the Pacenti rims because the top of the tire hit the bottom of the front brake. There was plenty of clearance in the rear. My main complaint about this bike is the angle at which the front brake attaches to the fork. If it were kicked back a bit, there would be loads of clearance. As it sits, the brake extends more toward the tire than over it, creating less space for the tire. I know that the issue is not just because of the TRP brakes. I purchased (and returned) a new set of Campagnolo Chorus brakes and the fit was no better. Luckily, I had a pair of Continental Ultra Sport 23c tires hanging in the garage. I'm not terribly fond of the red, but will ride them until I decide on a new set of tires. About a week ago, I sent an email to Jason Schumacher (Customer Service Manager) at Trek about the brake clearance issue, but haven't heard back yet.
I've only been able to get out on one ride so far with the new wheels, but they are fantastic. They are more stable in crosswinds than either the Boyd 38 or Mavic Ksyrium ES wheels and the wide profile really allows the tire to fill out and provide a nice ride on the crappy farm roads around Salinas.
The other new addition is the Ergon SR3 Pro Carbon saddle. It has a bit of a funky shape, so I need to play around with the position a bit before offering my opinion of it. The boxy shape at the front of the seat area pressed my hamstrings on each pedal stroke if I sat where I wanted to be. I'm going to move it back a little and drop the nose a little for my next ride on it.
Now that I'm just about done with this build, I need to figure out what other bike needs my attention. New wheels for the CX bike? Gearing change for the XC bike? Hmm...
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Update - October 23rd, 2014 - I have not heard back from Jason at Trek. By this point, I'm guessing I won't.