Being mechanically inclined definitely helps with these cars. I have always done a majority of my own maintenance and installs that don't involve a lift, which has saved time and money (and given me something to do on the weekends
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My car has had a few of the issues that are common for the N54 (HPFP, Vanos, and oil filter housing gasket), plus a few other minor issues and quirks. All were covered under warranty when they occurred, luckily.
Indy mechanic just means independent mechanic (i.e. not the dealership). Check out the regional forums for some good recommendations in your area.