Still haven't figure this out. The clicking has went from every now and then to happening almost on every start up now. Still goes away after a couple of minutes. I'm not very mechanical so I'm probably going to have a mechanic look at it.
Any other ideas on what could be causing this? I'll point out to the mechanic to check the areas mentioned above. Any ideas on how expensive this could be if it is something listed above?... or anything else?
Is there a Fram oil filter involved? If so, try swapping it with a good quality oil filter like Wix, AC-Delco Duraguard, Purolator PureOne, etc. Frams are notorious for leaking the top-end oil back down through the oil filter's check valve which allows a dry engine start.