I finally got around to testing things so I thought I'd share what I found.

First I jacked up the whole back end of the car and checked for any play. Everything was tight including the sway bar, control arms, bearings, etc. so I lowered it back down and jacked up the front end.

At first I thought I found the issue with the front end. I was shaking the wheel side to side and I felt and heard it clicking, but it turned out to be just the steering wheel moving slightly as I had apparently locked it when I got out of the car. Once I unlocked it and shook each of the front wheels quickly, I could not feel any play. Also, just like with the back end, there was no play in the sway bar, control arms or any indication of a bad bearing.

One thing I noticed that I think may be my issue is that as I was lowering the car on the passenger side, I heard a clicking type noise maybe 2-3 times that seemed to be coming from the strut. So now I'm thinking that this issue might just be that the strut is starting to go.

The reason I looked at the back end is that I've heard a noise from back there a couple times over the past few months which I'm now thinking is the shock mount on the rear driver's side.

What do you guys think? Is there anything else I should test?

Evan, it is possible that the shock in the rear has become loose. Get yourself a 10mm deep well socket and tighten up the nuts (2 of them up there). I know I fought a clunk for awhile before I figured out it was the shock that was moving about 1/16".

Yes, I'm thinking that may be the issue with the rear. Either that or it's time for a new mount or two.

But what do you think about the front? I heard that clicking noise only when lowering the passenger side front, I even raised and lowered it again to reproduce the issue and it did happen again. Could it be the strut? Or maybe some component of the srut?

Evan, can not help you with that. I would think that if the mount for the lower control arm was loose, you would end up with either bad tire wear or a really good wobble in the steering wheel.

Well I don't think that's the issue as both control arms were just replaced. Have you ever heard of a strut kind of "clicking" almost while moving? It's almost like something needs to be greased

The clicking noise?

On my car it ended up being the top of the strut mount which includes 4 pieces:

1-bump stop
2-spring seat
3-thrust bearing
4-top mount

I got all 4 items on ebay for $125 (each side) real jaguar parts from some online store in MI.

I had done so far on both sides in front:

control arms
stabilizer links
cv axles
rotors/pads
wheel bearings (cured passenger side noise)
sway bar bushings (this cured previous sounds)

Then got the click clack noise which got progressively worse as time went on..but the strut mount kit cured it and only took 45 min each side (if you have an impact wrench) and you need a spring compressor (I bought one at Sears for $55 for McPherson struts because it had the pins to lock on the spring)--my method was:

remove wheel
remove two 10mm bolts and one 21 mm for rear of subframe
loosen the 21 mm bolt at front of subframe but don't remove
remove two 15 mm caliper bolts and tie caliper out of way with ziptie
remove rotor
remove axle nut (32mm?) and push axle out of hub
remove top nut on stabilizer link (15mm and 18 mm wrench)
remove tie rod (15mm plus maybe a 4mm? allen socket to hold)
remove pinch bolt by ball joint (18mm socket and t55 socket)
pop ball joint off of hub--I found it impossible at first but came up with a 5 second method: take a 1" wide or so ratchet strap with a j hook on the end -- put the j hook on top close to the ball joint and wrap a loop around your foot about a foot off the ground--the secret is to stomp down quickly and it will pop right off...also is handy when reinstalling -- kinda can't get right but whatever works, right?
now
unhook the brake line grommet on the strut
unhook the abs sensor from hub
remove the three 13mm nuts from inside engine compartment and take strut assembly out (still attached to hub assembly)
use spring compressors (impact gun is great here)--you will see when the spring starts to lift off the bottom seat--just do each side a little at a time
use 18mm socket for the top bolt (needed impact gun)

Installation is reverse
You will need a front end alignment

Car drives quiet and much tighter I feel...

I had the strut mounts and bearings done on both sides so those are only a few months old. I did not do the spring seat or the bump stop though.

I can reproduce the noise I heard if I jack up the right front side and then slowly let it back down by releasing the hydraulic pressure in the jack. It sounds more like something is sticking and not lubricated enough when you're sitting right next to it.

Again, this seems to only happen in colder weather. The car is in the shop now for the latest installment of the ongoing transmission saga. The mechanics at AAMCO seem to think this issue is caused by bad struts and want me to have both replaced. The car is at roughly 65k miles at this point so it would seem they have reached the end of their life, however a simple "bounce test" suggests that they are fine. I'm not sure what to do at this point.