Quick update/FIX for anyone else having similar issues. I placed a go pro camera in the wheel well and was able to see the noise and thump was the passenger side. After a few different camera angles and road tests I can see the lower ball joint had some play when stopping and accelerating. I had put a pry bar on that when it was on the lift but with the suspension unloaded it did not move. I ordered a new ford oem lower control arm "Since you can not remove the ball joint, Crap design" Took it apart in about 30 mins and the ball joint was flopping in the breeze and able to lift up and down a good 1/4". Replaced it and all is well. Ordered drivers side also and will get it aligned.
Weird notes. It made no noise when it was below 85 degrees unless you drove it for at least 30 mins. Under no load car on the lift no noise when driving and no noise from a pry bar.