Interesting thread, I had heard of rear wheel problems, before I bought.I have had numerous problems with derailleurs, cranks, and rims. I have a 2006 Sequoia Elite.
No problems with the rear gears, but many headaches on the front. Throughout the summer, changing gears on the front was erratic. Sometimes the chain would fall off the lower chainring. Sometime I could not get it onto the large chainring. Sometime I would have to quickly shift up two gears in the front, to successfully get off the small chainring. Back to LBS many time for adjustment. Quite frequently, although somewhat erratic, shifting was very stiff, requiring almost all my hand strength to change front gears up. Finally, I had the LBS change the front deraileur cable. He commented that it was quite hard to get the cable out of the clip underneath the crank. Something about some black junk. The result. Oh my god, its a total different bike. I can change front gears with one finger. No more failed shifts. Just easy, smooth, consistent shifting, like the rear.
When the bike was new, I experienced problems with the chain skipping when peddling standing up. With less then 1000 km, I too experienced my left peddle coming off, and hanging from the bottom of my shoe. I didnt crash, but was wasnt quite sure at first how I was going to stop. The LBS reattached the pedals, and the chain skipping went away. During the last part of the summer, the bike had a shimmy, which I thought was coming from the rear tire. Then on a long ride, I noticed the crank shifting left to right. Tightened up the left crank, and the shimmy went away. The left bearing is now beginning to make some noise, and I have decided to replace the crank and bearings, with a Shimano Ultegra triple crank.
Around 1000 km, I started to break rear spokes, on the drive side. I am a fairly big guy, over 6 feet and 200 lbs. After the second broken spoke in a week, I had the spokes replaced with DT Champion 2.0 stainless steel spokes. Since then, I have not broken a single spoke. However, around 3000 km, the spokes began to pull right through the stock Alex rim. I guess the spokes were now stronger than the rim. The LBS recommended a Mavic Open Pro CD rim, with 105 hub. Since the upgrade, I have had no issues with the rear wheel. I have just decided to upgrade the front rim, to match the rear.
I too am using a Trek Interchange rack and bag. My only complaint is that the bag occasionally falls off. Its happened 3-4 times, and always when crossing railroad tracks. Its partially my fault for not connecting the Velcro strap, but I just assumed the rear clip would be sufficient.
I found the handlebar tape shifted forward leaving gaps. I removed the existing tape, and Bar Phat gel, and replaced it with Trek gel tape, and wound it very close above the brake hoods. No problems the rest of the season, and quite comfortable, even without the Bar Phat gel.
On the positive side, I actually wore out the rear tire, without a single flat.