Shaking 2009 Scion tC!
 

My battery went bad so I bought a new one. When I started the car it was shaking. (Like I was in an earthquake)
The window on passenger side doesn't roll down from the controls on drivers side & the sunroof is hesitating.

I need some help please... 2009 Scion tC

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Really hard to diagnose from that description, but shaking at idle generally means it needs new (OEM) motor mounts or you have a crazy vacuum leak somewhere. Could also be a voltage issue or a problem with a belt/pulley, so many things it could be.
Shaking while accelerating would generally lead to needing at least one new axle shaft, motor mounts or front suspension components. The other electrical stuff, could have something to do with the charging system.

Get an OBD2 scan and have the (new) battery and alternator tested to make sure your charging system is working properly.

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Changing your battery might force the computer to relearn your driving habits, (thus the rough idle.) The side windows and sunroof can be reinitialized. (Make sure your diver side window lock isn't engaged.) You'll also have to reset your radio station presets and "entertainment" screen.

1. POWER WINDOW CONTROL SYSTEM (WITH JAM
PROTECTION FUNCTION)
NOTICE:
• Resetting the power window motors (initializing
the pulse sensor) is necessary if: 1) the battery
terminal is disconnected; 2) the power window
regulator master switch, power window regulator
switch, wire harness, power window regulator and
power window motor are replaced or removed /
installed; or 3) the GAUGE fuse, AM1 fuse, FL
DOOR fuse and FR DOOR fuse are replaced. The
AUTO operation function, jam protection function
and remote operation function via the power
window regulator master switch will not operate
unless the motors are reset.
• Be sure to reset the power window regulator
motors using the power window switch on each
door. The motors cannot be reset by remote
operation through the power window master
switch.
• In order to prevent a large amount of current from
being flowed into the system, do not
simultaneously reset 2 or more power window
regulator motors.
• If the power window switch has been
continuously operated for a long time, the power
window regulator motor will stop so that no
additional load can be applied to the motor.
Continuing to operate the switch even after the
motor has stopped will cause the switch to blink
while restricting the AUTO UP / DOWN function
and the remote UP/DOWN function. If this
happens, reset the motor again after a few
minutes have passed.
(a) Turn the ignition switch ON.
(b) Halfway open the power window by pressing the
power window switch.
(c) Fully pull up the switch until the power window is
fully closed and continue to hold the switch for
approximately 1 second after the power window is
fully closed.
System Name
Power Window Control System (with Jam Protection Function)
Sliding Roof System
INTRODUCTION – REPAIR INSTRUCTION IN–25
IN
(d) Check that the AUTO UP / DOWN function operates
normally.
HINT:
If the AUTO/DOWN function operates normally,
reset operations are complete. If not normal,
perform the following 3 steps below.
(e) Disconnect the negative (-) battery terminal for 10
seconds.
(f) Connect the battery terminal.
(g) Perform the first 4 steps above.
HINT:
If the AUTO / DOWN function operates normally,
reset operations are complete. If not normal,
perform the following 4 steps below.
(h) Turn the ignition switch ON.
(i) Halfway open the power window by pressing the
power window switch.
(j) Fully pull up the switch until the power window is
fully closed and continue to hold the switch for
approximately 12 seconds after the power window
is fully closed.
(k) Check that the AUTO UP / DOWN function operates
normally.

***********************************************************************************************************************************

2. SLIDING ROOF SYSTEM
NOTICE:
The drive gear (motor) must be reset (pulse sensor's
location must be set) when one of the following
occurs: 1) the battery cable has been disconnected
from the negative (-) battery terminal, 2) the drive
gear connector is connected /disconnected, or 3) the
sliding roof is replaced or installed / removed. If the
drive gear is not reset, the AUTO function will not
operate.
(a) The sliding roof AUTO operation and the jam
protection function may not operate normally if the
battery cable is disconnected / reconnected, the
battery replaced or recharged. Initialize the sliding
roof system using the method below.
(1) Turn the ignition switch ON.
(2) Press the CLOSE switch to activate the close
operation. Fully close the roof and continue to
press the CLOSE switch for approximately 2
seconds. When the sliding roof control ECU
initialization is finished, the roof will
automatically open and stop a few millimeters
from the fully open position.
HINT:
If the battery cable is disconnected, the sliding
roof control ECU may not detect the position of
the roof glass. If the sliding roof AUTO operation
is still disabled even after the drive gear has
been initialized, the Hall IC may be
malfunctioning. The Hall IC is built into the drive
gear and detects the roof glass position.