So the saga continues, and I finally got back all my three lenses with the Nikon D90 today. All lens were calibrated with the body now and the sensor is now spanking clean after a thorough sensor cleaning via liquid solutioning. I am ready to do some serious shoot again after that whole one week of not doing so. This coincidentally matches up with the upcoming public holidays in my country. O yes!
As for the front/back focusing discrepancies I encountered, I am specifically told by the Nikon Engineer that I should engage AF-S mode to avoid unintentional recomposition focus error. Manual selection of the 11 AF points are still preferred after all. Hmm...so much for using AF-A all this while.
Lens calibration will become a need as the lens wears down and remains more of a want for me at this point of time. I was told that for my case, the re-calibration was but a very small marginal reset. Anyway, better to do this every 6 months, being still within the warranty period.