The smoke is probably oil leaking down onto the exhaust manifold. When installing the valve covers (cylinder head covers) the procedure is as follows:
1, Clean cylinder head cover and both sealing surfaces. Inspect and replace gasket as necessary.
2. Install cylinder head cover and hand start all fasteners. Verify that all double ended studs are in the correct location and install ground straps. The ground straps must be installed in the same location as removed. The covers are machined to accept the ground straps in those locations only.
3. Tighten cylinder head cover bolts and double ended studs to 70 in. lbs (6 ft lbs). Begin torque sequence in the middle of head cover and torque bolts moving outward in a crisscross pattern from top to bottom.
When installing the exhaust manifold:
Clean mating surfaces on cylinder head and manifold. Wash with solvent and blow dry with compressed air. Install the manifold gasket and manifold. Install manifold bolts and tighten to 18 ft. lbs.
The check engine light and flashing lighting bolt are probably for the throttle body. Check the wiring harness/connector to the throttle body and the engine ground strap that's connected to the engine head cover. When removing the electrical connections, did you disconnect the main battery negative cable before disconnecting the electrical connections? If not you may have several diagnostic service codes logged. Plug a scanner into the car's OBD2 port and clear all codes. Then check to see if any new codes are logged. Sometime a ETC Relearn (ETC = electronic throttle control) is needed after disconnecting/connecting the electrical connection to the throttle body. The dealership uses a diagnostic tool to perform ETC Relearn, You can try the following procedure to see if it works for you.
ETC Relearn:
1) Push start button to "Run" (older models insert ignition key and turn to "On") ... but do not start engine.
2) Wait for all idiot lights to go out. Check Engine Light may remain on.
3) Slowly depress the accelerator pedal all the way to the floor and hold for 10 seconds.
4) Slowly release the accelerator pedal until it's all the way back up.
5) Wait 10 seconds and turn ignition "Off"
6) Start the engine.
Without the diagnostic tool the 10 seconds hold/wait time is an estimate. The diagnostic tool tells you how long to hold and wait but it typically is within 10 seconds.
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