I started having problem with my 2000 Audi 4.2 misfiring and shaking real bad when I start cold
about 2 weeks back. If I turn off the motor and re-start this goes away. I am also experiencing
very minor hesitation when I press gas pedal after stopping.

The dealeridentified fault code 17549 - Load Detection Implausible Valve and came up with
an estimate to repair intake manifold with $2,000 estimate. I need advice from experts or
others who have had similar issue and also whether this diagnostic by the dealer is accurate
or they are taking me for granted. I will appreciate any insight. Lately I have been having numerous
issues with this car costing me roughly $4-5k repair expenses every year for the last three years.

 

The cold start misfire is probably a bad coolant temp sensor.

As for the fault, what are they going to repair? Replace intake manifold gaskets? Thats a posibilty. You could have a vacuum leak, or it could be a bad mass airflow sensor.