I expect that you are aware that it is an interference engine, and serious damage can occur if the engine is turned when the timing is not correct.
16825/P0441/001089 - Ross-Tech Wiki
16795/P0411/001041 - Ross-Tech Wiki
Your current problems are not caused by the alternator, but if it is noisy it should be replaced again.
V6 TIMING BELT REPLACING
When you do the timing belt, I suggest you replace the following:
A) Timing Belt
B) TB Tensioner Damper
C) TB Tensioner Roller
D) TB Idler Roller
E) Water Pump & Gasket
F) Thermostat & "O" Ring & maybe the Housing
Also consider replacing:
G) Serpentine (Accessory) belt
H) Serpentine belt Tensioner
I) Check all coolant hoses, replace if required
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V6 CRANK LOCK PIN
The crank must be exactly at #3 TDC to get the crank lock tool in correctly, it
should screw in easily. Move the crank back & forth a little
to get it lined up, while screwing the tool in. If you have difficulty, check that #3
is at TDC, if not turn it to TDC and install lock tool.
See pics in this thread:
http://www.passatworld.com/forums/42-volkswagen-passat-b5-discussion/392186-crankshaft-locking-pin-tool.html
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V6 TIMING BELT
Instructions for V6 Timing Belt replacement.
I suggest you carefully, and precisely in the order listed:
Disconnect negative battery cable.
1) Turn the crank to TDC. (Cylinder #3 TDC)
2) Compress the tensioner using an Allen wrench (clockwise) in the tensioner roller, and fit the pin in the tensioner.
3) Remove the Timing Belt.
4) Turn the crank counter-clockwise to about 45 degrees before TDC. (valves can't hit pistons in this position)
5) Remove the cam pulleys, and refit leaving them just loose enough to turn freely.
6) Then use the cam lock bar to turn the exhaust cams so the large holes in the pulley plates are facing inwards (toward each other), and fit the cam locking bar.
6a) Re-check cam chain timing, correct if required. (Not necessary if chains haven't been touched)
7) Turn crank clockwise to the timing mark on crank pulley, and fit the crank lock pin.
8) Fit the water pump, thermostat, tensioner, idler roller, and tensioner roller.
9) Fit the TB on the crank pulley first, then working in a counter-clockwise direction, fit it around all the other pulleys.
Make sure the belt is tight everywhere except the section that goes over the tensioner roller.
10) Release the load on the pin in the tensioner with an Allen wrench in the pulley (clockwise), remove the pin.
11) Allow a couple of minutes for the tensioner to extend, then pretension the TB, using a torque wrench in the tensioner roller turn counter-clockwise to a torque of 132in-lbs (15Nm).
12) Tighten the cam pulley bolts to 41ft-lbs (55Nm). (With cam bar still installed)
13) Remove the cam locking bar and crank lock pin.
14) Carefully turn crank 2 full turns back to TDC and recheck timing.
15) Put the rest of the car back together and go for a drive.
If you have any concerns about this, please ask before proceeding.
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CAM CHAIN TIMING
If any cam has been, or is going to be removed.
Disconnect negative battery cable.
A) After setting the crank to 30-60 degrees before TDC. (See above) Install the cams and set them to the timing marks with the chain fitted correctly. (16 roller count see diagram)
You can fit the cam pulley holding plates to the exhaust cams, and use the cam locking bar to turn the cams.
B) After all 4 cams are correctly aligned to the timing marks as in photo, and the chains are correct. Fit the cam locking bar.
C) Turn the crank clockwise to TDC and fit the crank lock pin.
D) Fit the timing belt etc.
Check the pics in this thread to see how you can have the chain timing wrong with the timing
marks aligned and the bar installed.
http://www.passatworld.com/forums/b5-garage/387417-30v-v6-cam-chain-16-links-take-look.html Post #1 Timing is wrong, Post
#8 Timing is correct. (This is bank 2)