I think the most important thing is to relax as much as possible when you do the things that make your joints pop/grind so that there is a minimum of tention in the joint. Also stop lifting weights as that will make your muscles more tense and make it harder to relax. Try to lower your shoulders as your hands go up to cut, instead of raising them. Raised shoulders = tension in the joint. This will also make your arms go up more directly in front of your face to create a better shield. Also when your thrusting straight forward (tsuke) keep your shoulders relaxed. Bruce Lee once said: "A correct punch should see the arm completely relaxed until the moment of impact. And have a snap several inches behind the target."
I hope your problems will not hinder you in your training, and that they leave you soon.