Have its clunking when you send torque through the system it could be a couple of things, none of which I've ever checked on an s13.
transmission mount, if its going the transmission could be clunking from being torqued.
Maybe something with the rear as well, driveshaft u-joint or even wheel bearings in the rear.
If it feels like its coming from under you, check the transmission mount. (if this is not possible for those reading please correct me)
I for some reason doubt its your subframe bushings with those miles on the car...still possible though.
Edit: going by what someone is calling a clunk is very hard to diagnose, because we all have at times different 'classses' of clunks
