I think you'd best prepare for the worst and hope for the best. Just remember that the CMs have guest safety in their minds first and foremost, so be kind if they do not let your son on specific rides.
Honestly you may even run into situations where he measures at 40" one day and not the next. If this happens, try to take it in stride. There's really no point in arguing with the CMs. They would much rather have one disappointed child to deal with rather than an injured child who was too small for the safety restraints. Most CMs deal with it very well, and you may even see one of the certificates that welovedis mentioned.
On a personal note, if your son does measure up to the 40", you might want to be a little cautious before jumping on Dinosaur with him. Even as a 32yo adult, I think that is one of the most physically abusive rides at WDW. It really jerks you around throughout the ride, and has the added elements of dark lighting and frightening dinos jumping out around each turn.
I'm with you on TOT and Splash Mountain, and even BTMR. But you might want to ride Dinosaur yourself once before you subject your son to it.
Best of luck.