@Sam-I-Am Good move having him take Chem - I think MIT requires 1 math and 1 science subject test, so the Lit would not have been helpful there. Good luck and let us know how he did!
Have your son email admissions or call. They will head you in the right direction!
Please be sure to provide an update on how it worked out for your Son (3/14/17, I assume, will be real close to the MIT admissions announcement date). My kid went through a similar internal debate after scoring 35.25 on the ACT. He went ahead and took the ACT one last time due to coming so close to a 36. He was literally losing sleep over this. It worked out.
@kmccoy, Funny but that is my kids ACT score as well. Took it a second time because school offered it during the school day at no charge (basically was required). Did not retake the ACT merely to raise score to 35.5 and get a 36. Most assume a 36 means “perfect”, but as you know they round up the composite score if the average is at least 35.5.
The thing about these test is I already know more content and most of the question is easily solvable specially math 1 but I can’t get a good grade at them 
I think that is a common problem with kids taking AP Calc and even Calc 3, then trying to do well on the math subject tests. That has been a concern I have for my kids. I wish they had written the subject tests immediately after doing the coursework.
The MIT published scores for the middle 50% on the math subject test are 780-800. See: http://mitadmissions.org/apply/process/stats.
They don’t mention the distribution of Math I and Math II.