Is your car a manual or auto? If I read what you posted correctly, you installed the konis and the clunking started. Could be the konis that are causing the noise and issue. Other people I've known that have konis as well report similar issues.
Otherwise if you have a manual, that noise would be normal when you're engaging/disengaging the clutch and shifting gears. Mustangs do make a lot of noise.
I do drive a manual but I don't think it's tranny noise. Only happens on bumps and potholes, etc. :/
When I had a clunk in the past it was due to something not being tight enough. Twice I have had my sway bars work loose causing a clunk/pop sound. Maybe see if a fellow lister here is close and give it a second set of eyes to check everything??...
Yeah my searching of forums lead me to everyone saying it's the endlinks. But unfortunately, doesn't seem to be the case with me.