It took quite a while to relearn the adaptions when I replaced the solenoids and upper seals on my 04 4.4i. I only drive it a few times a week. IIRC, it took about three months until the shifts were really smooth again. Maybe not exactly what you're seeing, just sharing my experience.

Adaptations transmission
 

Thanks haigha, great info. I checked the readouts in INPA again and the O2s seems settled now, cam values look good. The engine runs smooth and I am pretty sure any hesitation left is the transmission shifting.

Now that I am several days in to this and the car has been driven by three different persons over varying stretches it seems the trans is slowly catching up. This morning I did another 25 mile round trip with it and it seems to be fine with only occasionally a slight hesitation that most people would actually not perceive as such. So, I am pretty sure that this is the same effect as haigha mentioned.

I feel confident handing the car to my kids again, there seems to be no running problems left. It was aligned last Friday and the shop was so hesitant that I wondered if they had actually worked on it.....this morning I discovered a long 16-18mm ratchet wrench left in the car, free gift I guess. So, somebody worked on it for sure :-). It steers straight and true so no complaint there.

Ordered a Dremel to make some changes to my modded headlights so I can install the Morimotos. Once I am sure that works I will order a set of LED projector for the high beams. The OEM light units that are installed now are terrible despite my efforts to polish them. I guess early 2000s lighting was not that great.

A good cleaning inside and out and some wax will complete the job. I still enjoy this car a lot as it has a handy size and is good for getting through the dense traffic we have here. A few lingering items are putting a new hatch handle in and replace the TLDM which I have had in the garage for months (it rarely throws a CEL).