Okay so what am I missing here? I managed to pry one of the caps out after removing all of the clips but the others are proving even more resistant - what am I missing here?

Bill

sometimes they need to be pressed out.
rust seems to keep ahold of the caps

A large socket fitting the yoke and a smaller socket fitting the jU-joint cap opposite of each other. Fit the assembly in a large vice or press and press the cap into the large socket. Same for the other yoke if slip yoke.

Assembly is reverse after using some crocus cloth to clean the bore and grease the outside of the caps. You might even insert a stay bar between the yoke to prevent offsetting the yoke during the install. Lube the joint after install.

Place the zerk between the driving yoke and driven yoke, the compression side under power.

I haven't done it, but my driveshaft shop takes a big 3 lb hammer and slams the bejesus on the yoke. He says it stabilizes the joint within the yoke. It does have a nice ring to it when hit.

yup, what he said, 2 sockets and a vise.