I am sorry your son has had to go through this at such a young age.
I am afraid it is fairly common after this type of surgery to have frequent loose stools, I am in double figures but I have had nearly all my bowel removed.
There are some medications and things he can do to help which his Dr can perscribe and other things to concider.
The job of colon is to suck the last of the water back out of your poo and that job is reduced by the removal of some of it. The small bowel also helps this job sucking out the nutrients, vitamins and minerals too.
I see you son is on methotrexate and Folic is he also on something like Pentsa?
One of the problems with losing so much of the small bowel is malabsorption, there is not enough left to do the job properly. Nutrients, vitamins and minerals can all run low and lead to other jobs in the body not being done efficiently.
Your son is very young any deficiency he may have is worth picking up early for his long term health for instance, Vitamin B12 is only absorbed in the terminal ileum, the part of the small bowel that he has had removed.
Vitamins and mineral play a big part in how we function and some of the loose stools could be due in part to some of these vitamins and minerals not being absorbed or indeed being lost due to frequent loose stools.
As he is on methotrexate he should be having regular blood tests, I would advise you to ask your Dr to do a full blood count along with his next bloods.
I hope this is helpful, Good Luck