This may sound daft but DS was just 40" when we went in July but I found that he was taller in the morning than by late afternoon

so we tended to do the 'big' rides first thing. Obviously we literally walked the feet off him!
We found the CMs to be very precise when measuring, and at one point they had a credit card that they slid between the bar and the child's head to see if there was a gap. The only one we had any problems with was Soarin'. He was OK for the height limit outside, and we checked during the queue, but when we got to the boarding area, they re-measured him and he was too short and could not ride. The CMs were fantastic with him - they explained that he wasn't tall enough, then took him and showed him the big screen and told him what his Mum and Daddy would see on the ride, so he didn't feel he'd missed out.
Good luck with your son's height, my DS loved Splash Mountain - it was his favourite ride - he is still asking to go on it now!
Sara.