re: "...When I put the car in drive after sitting over night (Cold) there is a long hesitation (about 3-4 seconds)then in bangs into gear...."

Now, noting the long hesitation, it sounds even more like low fluid level. I would also have suspected old contaminated fluid had you not already mentioned that the fluid was flushed just a couple of tens of thousands of miles ago (in either case, fluid isn't circulating properly and pressurizing the system at first), but now discounting that, it seems that the fluid level is going to be the most probably answer; as the fluid warms, it expands and the level rises, so it doesn't reoccur until the next cold morning.

So check the fluid, but be careful which temperature scale (side of dipstick) you'll use (remember the link I gave you about temperature and fluid level).

Hope this helped.