My oldest daughter has always been tall for her age so I understand your dilemma. We did let her ride Barnstormer first to gauge how she would handle things. She rode it several times so we moved on it BTMRR. She loved it, too. Then we tried SM and later Soarin'. Uh oh! She hated them. We finally figured out that she loved speed and heights, but couldn't handle darkness.
She is now sis and tall enough to ride everything, but we won't let her do Space Mountain, Mission:Space (easy side), or RocknRollercoaster because she still has issues with things being dark, and I don't want to chance it when I can't help her.
Good luck and just go slowly with some of the easier things like Barnstormer and Soarin' to see how he handles it. I would avoid any of the intense rides at his age even if he is tall enough. The height requirement for ToT is only 42inches, but I think the storyline is a bit too intense for most children. We finally let my daughter ride it last year when she was 5 (actually DH allowed her, not me), and I think it was a pretty bad idea.