Well I have mine in the shop today for the Tranny noise and the "clunking" noise. I am not too concerned as of yet with the tranny noise but the clanking noise which is repeatable by slowly driving over a speed bump "Clank,Clank" I am. I went on a drive with the shop foreman and he thinks it is front suspension related. I called back after a few hours to get the status and was told the lower control arm needed to be replaced and that the parts will have to be ordered.
I also went on a drive with the shop foreman in New same model Focus with 12 Miles on it and it is noticeably different like no clunk and Quiet.
I'll post back after the repair and inform on the results.
Here is my invoice for today looks like only the left strut needs to be replaced. Will see?