cmjw11

Lower control arm With ball joint and bushings didnt fix the problem, just muddled the clunk down a little bit

rflynn1

Take it to a Mazda dealership.

No offense, but if you haven't figured it out in 2 years, and have spent countless hours and resources attempting to find the root of the issue I doubt you are going to any time soon

Wolveger

You may have one or both main shafts loose in transmission. The shafts loosen and the splines will have a little play in them, when accelerating and braking the splines are in contact and won't make noise, when cruising, especially in cruise control you're car is constantly going into accelerate/decelerate mode so the splines are constantly moving back and forth making the clunking noise. There are some greases out there which help cushion the "spline slap" and then there's always the more expensive route of trying to replace the main shafts in hopes of getting a slightly tighter tolerance, if this is the case that is. I would start off with the grease, if that quiets it somewhat go from there.

NasTHatch

have you checked the Rack and pinion to make sure it's actually tight? if it's not secure it can shift, same thing with the sway bar frame bushings, they wear out and the sway bar shifts back and forth