It's easy to get carried away in search of perfect blacks, but that can result in some significant loss in shadow detail (at least for the D series, not sure about the E). With the right equipment, you can get around that by calibrating to a custom gamma curve.
But with or without a custom gamma curve, I like to use the APL clipping pattern on AVS HD 709 to set brightness (helps to prevent you from setting it too low), and if I still feel like I'm losing shadows I will raise brightness to just barely see bar 16 flashing from my viewing position. That's a loss of MLL in exchange for full shadow detail, but I want to see everything in the image.
There is no evidence of any magical picture enhancement from breaking the TV in. I'm sure someone would have measured it around here if that was the case. Basic calibration settings (bright/cont/color/tint) will probably not change much if at all. Advanced calibrations (color space and grayscale) are known to drift more in the first 100 hours or so, and need to be checked every 500-1000, but this is for the pros (and DIY cal crowd).