Noises During Shifting problems of the 2009 Toyota Tacoma

Purchased new Toyota Tacoma trd sport in Aug 2009 with zero miles. All seemed ok, other than a few frustrating cab rattles here and there. However, I also noticed that as my truck neared more miles (7,000 current), I now have to press on the brake pedal a bit harder, yet when I brought this up to the dealer, they stated all was normal and could not replicate. I've had a couple of instances where I've had to press the brake pretty hard to come to a stop or slow down. It seems I need to ride it a little harder than when I first bought my truck. I also want to add, that besides the irritating rattles (door panels/tray holder in center console below the steering wheel - which was replaced, but still make pop sounds here and there, the other smaller rattles - some of which were coming from ill-fit window seals were not really fixed. The dealer replaced the seals and the popping sounds stopped for a day or so then returned. I found the problem is the seals tend to be somewhat improper fit. In other words, they are too large and cause the rubbing. I personally corrected this by removing all door panels only to find out that some of the rattle sounds I had complained about merely had a small piece of felt on the backside, which did not completely cure the problem. I purchased an entire roll of this material myself and coated the inside of each door panel then added a small piece of weather stripping to the inside of door panel edge where it touches the glass window. This helped considerably in reducing air noise and no more rattling. My complaint is still with the brake pedal sometimes, not always, needing to be pushed harder than normal to come to stop or slow down. On other thing I addressed with the dealer was the fact that when I slow down and make turn, not complete stop and go, my engine rpm's don't decelerate quickly enough for the transmission to catch up. Dealer states this is normal operating rpms catching down to shift down of tranny.