Hi Dankowen,
Your feedback is helpful. Judge the effect of running by how long you have pain for and whether or not you have swelling or redness around the joint. If you have pain for over two hours post running, you may need to reduce the intensity of the run. Sometimes correct taping of the area can spread the load over a wider area whilst supporting the injured region.
It may be that the joint requires more mobilisation and massage. As I have said, it can be a slow process. Non steroidal anti inflammmatory gel application may also be of benefit, as would pre and post run icing for pain and inflammation control. If your symptoms disappear within 30 minutes post run you should not be causing any significant problem. If you have aggravation from a run into the next day, back off the run intensity. A different type of running shoe can sometimes assist, but that can be an expensive experiment. If you are using a light weight running shoe you could try a cross training shoe with more support. I prefer minimalist barefoot running type shoes eg Nike FreeRun or Vibram 5, however barefoot running shoes tend to have runners spread the load more through the mid and forefoot which is usually a good thing, but not if you have a sore toe!
Contrast baths for swelling can reduce pain eg 20 seconds in ice slush then 20 seconds in warm water (not hot) repeated 5 times twice daily. If you have minimal swelling, do not bother with this technique.
Good luck.
MrPhysio+