I've often had popping jaw, clicking neck when I talk and knees in the past. I did at times have knees so sore than I struggled to walk but that all stopped ages ago. I haven't eaten gluten in 4 or 5 years and I guess it stopped about then. By the way I started getting regular B12 injections about then too. I'd recommend you start having the injections especailly with your restricted diet and low weight. Cold hands and tingling is CLASSIC B12 deficiency. Id also want to know why your stomach in inflamed, yes sure maybe your small intenstine could still be but your stomach shouldn't be after a year on a good diet. You want to have a test for helicobacter while you are there.
If there's anything to say about the popping itself (if it doesn't hurt I think it's zero problem). I've been told many times by Europeans when I was younger after they have heard my knees pop that I must be very healthy :! apparently in Europe the old tale is, if your joints pop they are in good condition.