So when I'm in the drive thru or just have my foot on the break there's a really loud clunky sound that vibrates the car. And when it's in park it sounds like it's going to shut off. From what I've read could it be collapsed motor mounts? Or does the throttle body need cleaned? Or is it something else?

 

It could very well be your motor mounts. While you are at it, just clean the maff, ESS, clean the intake box as well your filter could be saoked in oil due to overflow, cleaning throttle body never hurts be carefull though rx8s have electric TB either take it apart and clean front and rear or just clean the front don't twist the butterfly in the middle..
Also, make sure your plugs, wires and wires are not old.

 

Is it making those noises on startup as well?