Clutch issues

I just recently got my 2013 on the 12/22. Each time I press on the clutch and release I hear and clicking/popping noise while in neutral and a little louder when shifting. At first I thought it was due to the break in period and all that stuff, but I am a little worried. I have been driving stick pretty much my whole life and never had an issue like this. Plus while in a stop light I get a thump, it was occasional, but mow it seems to be happening more often. I don't know if I am expecting it to be completely perfect since it is a new truck or its normal.

 

Mine doesn't do any of that.

 

Clicking and popping noises from the transmission when shifting gears is normal. The Aisin trannies are noisy boxes to say the least. The clutch itself should be quiet, with the exception of the plastic pedal plunger under the dash; that bugger will start creaking down the road until you spin it back and forth to smear the grease around again.

For bumps at stop lights, check your u-bolts on the rear springs. Toyota is notorious for under-torquing them. When they're loose and you slow down, the axle wraps forwards too much, and when you let up on the brake pedal a little after stopping, the axle springs back and makes a THUNK sound/feeling.