I'm not sure what could cause the motor to jerk, but as for the brake pedal feeling like it sinks a little after you stop, do you hear an audible change in your radiator's fan speed when it happens? My 2nd gen wagon does this at stop lights. I don't know the true cause of it, but my brake pedal pressure correlates to what the fans are doing, weird as that may sound. I thought it was a side affect of the load on the engine when some new accessory (ie the fans) spin up.
Either way, it sounds like you're still well within your warranty period to have them look at these things.
Either way, it sounds like you're still well within your warranty period to have them look at these things.