There are some things we don't know or at least I don't. What size are you? What are your short and long term baseball goals?
It seems to me that this guy is trying to help you find a way to stay relevant as a pitcher. He is trying to find you a technique with guaranteed movement because you lack velocity. I know your velocity is improving but it is still below what you need for the next level. How effective are you now against your competition? Does your arm hurt because of the slot or because of the arm action he is teaching you? Do you buy into the lower arm slot? Could you raise it up some, maybe neutral sidearm and retain movement?
Can you tell him your arm is hurting and ask what he thinks you guys might do to help you maintain movement while taking some pressure off of your arm? The sub slot does provide an unusual visual presentation for the batter and sometimes wicked movement but it is not easy and usually only effective for short stints.
You need to let him know that arm action is painful but you should also be open to finding methods to be deceptive as a pitcher.
Has your arm pain abated and how does your arm feel when you throw from your more developed slot?
Good luck,
Ted