Not sure about clicking joints but i used to have a young horse who sufferd from a locking stifle, now that was really scary, first time it happened i thought she had a broken leg, would literally drag it along behind her, after about five minutes it would unlock itself and she would be fine! By the time she was about three and a half it had stopped happening, it's apparently not that uncommon in young horses, so maybe the clicking thing is just something similar?
Cod liver oil won't heat him up at all, any oil is a slow release energy source and shouldn't cause any adverse side affects at all, hope that helps