Pre-94 (and some early 94): The shifter coupler is a rubber piece with two 10mm nuts on each side. Pictures. You can get to it by leaning way over the engine from the front and looking down behind the engine. A bad coupler is the root of most severe shifting problems (inability to engage a gear, not gear grinding, which is usually bad synchronizers).
The clamp bolt is for adjusting the shifter (not really recommended, as it's really touchy).
Mid-94 and onward: The coupler is essentially two concentric vertical pipes separated by a rubber sleeve. The outer housing has a horizontal pipe that couples to the shift rod from the passenger compartment. The inner vertical pipe is connected to a horizontal pipe that connects to the transmission shift rod. The outer vertical housing (hub/whatever you want to call it) has an opening for the horizontal pipe to come in from the transmission side. Pictures. This coupler doesn't fail like the earlier one, although if oil is allowed to leak onto it, the rubber will deteriorate and cause rattles. If it deteriorates badly enough, it probably could cause some pretty sloppy shifter operation.
This thing would be a cast iron bitch to replace normally, I would think. It's hard enough to do when the transmission is removed, and I absolutely recommend replacing it if you do have the trans out. To remove the taper pin, loosen the nut with an 8 mm box end wrench and back it off 1/8" or so (make sure the outside of the nut moves beyond the end of the stud). Now you can whack the hell out of the nut with a hammer until the taper pin finally pops loose. This may well ruin the nut and/or the pin. Now remove the nut - the threads will probably be boogered up and you'll have to grasp the other end of the pin with ViceGrips (that's not an easy thing to do either!). It probably would be much better to Superglue a nut (3/8" or so) to the fixed part of a C-clamp, then slip the nut over the end of the taper pin and tighten down the rotary end of the clamp on the nut until the pin pops loose. Much easier, and much easier on the pin, I suspect ... wish I'd thought of that before I took a hammer to it. If you do use the hammer routine, you should replace the pin and nut (a few bucks).
Before removing the clamp on the other end, scratch or paint a mark in the channel where the tube is split. You can easily judge the depth to install the new one by the cleanliness of the rod (you'll see what I mean after you remove the coupler), but you do need to mark where the channel is.