Get a good ball peen hammer and punches (sometimes called drifts) to knock out the portion of the shear bolt that is stuck in the PTO shaft. Keep the ball peen hammer, punches, wrenches to install the shear bolts and of course the shear bolts with you when you are in the field using your cutter. Be glad that the shear bolt did it's job and broke. Do not be tempted to use a higher grade bolt! Think of what would be happening if the shear bolt didn't break and something a lot more expensive broke, like your tractor-it won't always be under warranty.
Regarding the JD or Land Pride Quick Hitches, I've had both. Started with the JD, but thought it would be better to have the Land Pride for additional flexibility on some of my attachments. From my experience, the Land Pride is heavier built, but is less tolerant of adjustments than the JD. I probably should have just had my attachments modified to fit the JD, but it's really not a huge deal. But with both, you must use the correct bushings to work as advertised. It appears from a couple of your pictures that you do not have the correct bushings to fit the link pins. As you noted, get that right and you'll find it should work as it should. For me, a quick hitch is a must.
Read the manuals. Then go read the manuals. And then go read the manuals. I'm joking a little here to make the point. At some point the salesman won't be available, and you will have to learn the finer points of setting up and operating the equipment. That and time and experience will help you get the most out of your equipment. You've got a nice set up, and you'll soon find it will get to be easy. Good luck!