I get similar pain issues, but I relate it more to barometric pressure changes. The recent weather's drastic weather changes have been really bad for me.
Remember, this is all just a theory on my part. When there's all the bad stuff in our cells, sometimes our bodies don't regulate the blood-cell barrier well. The bad stuff keeps the cells from functioning properly. So when the barometric pressure changes, the cells can't let in and out what it needs to to adjust to the change, so we experience pain on a microscopic level. Think of squeezing a balloon ... if there's no release of pressure, it feels like it is going to pop.
For me, it feels like a deep down ache, all the way down into the bones. This is not in the joints. No pain killer really helps, nor any supplements I've found. Sometimes heat or the weight of heavy blankets will comfort, but won't help. I know a lot of people when they get this just say it's arthritis, but it's not. And doctors can't explain the barometric pressure pain ... they can't truly test it because it is on a microscopic level.
The only thing I've ever discovered that helps is doing a salt push or two. My theory here is that the salt helps the cells allow things in and out, thus allowing them to self-regulate cellular pressure. Which also (the thing that those of us on Iodine love) allows the chloride IN to bump out the bromine or any of the other bad stuff so that the Iodine can then displace the chloride.
I have noticed sometimes when I'm taking a lot of Iodine the barometric pressure pain can increase, but I'm thinking that the Iodine has gone in to the cells but what it's displaced can't exit because my cells aren't regulating the cell barrier well. Thus the salt push and the relief from the pain.
When I'm experiencing the barometric pressure pain and I do a salt push, I will experience enough relief to sleep within about 20 minutes of the push. On occasion I will have to do a second push. The weather here in the Midwest (United States) recently has been drastically changing the last few days (temperature drops from 50°F down to 20°F within a matter of hours, then a couple days later the reverse). I've had some of the worst barometric pressure pain ever, and I do blame it on the weather. Salt pushing helped. Pain killers did nothing.
This may or may not be what you are experiencing, but I would recommend trying a salt push. If this isn't what you are experiencing, you may just be having a Herxheimer reaction, and a salt push would help with that, too.