I too am a father to a child with a venous malformation. From your post it sounds like your son has developed a blood clot which can be very painful. My daughter develops these clots often and they are always on the bottom of the foot.
I'm no doctor and your experience may differ but we have found that a warm bath, day after day, really helps dissolve the clot somewhat. Also, we have found that cold surfaces, or cold temperatures in general, increase the frequency of these clots. My daughter wears a soft slipper indoors that helps with pain when walking.
Also, like you, I was hit very hard emotionally realizing my child had a serious condition with a lot of unknowns and anxiety. My advice to you is to do what it takes to lift your state of mind. Find a way to be a proverbial "rock" LOL. Also, try not to let him see your sadness. That little guy is counting on you more than anyone.
As for treatment, it seems you have already done your homework. A lot of options are available but they are only treatment and temporary. Dr. Yakes does claim the word "cure" but at great cost financially and physically as he does as many serial ethanol sclerotherapy sessions as it takes to get a clear MRI.
I plan on trying foam STS sclerotherapy before I entertain any notion of Yakes. Partially because of the risk and partially because Yakes will cost me 500 grand (OUCH!!)