I agree with everything ReneeQ said. I took my 5yo sister last year and we are going back at the end of March. Since it is a special thing for us to do together I adopted a mindset similar to ReneeQ's. The trip was for her, my fun was in taking her and experiencing things with her. I made PSs were I thought we would have the most fun, but if we didn't make it, that was fine too. I made her an autograph book and we hunted for characters. We rode only the rides she wanted to (I can always go another time and ride things I want to). The only things she wouldn't/couldn't do were Space Mountain, RnR, Tower of Terror, Dinosaur, Tough to Be a Bug, Honey I Shrunk the Audience - if he's a little braver or taller, he may love any or all of these.
My best suggestion is to make a basic plan, but let him have the lead from there. I decided in advance what parks we would go to on what days, or at least where we would start, and also breakfast for each day. At the parks she would decide which direction to head in and what to ride. The choice was also hers to rest or change parks (and which to change to). She was allowed to eat whatever she wanted, whenever she wanted (knowing she wouldn't opt for all ice cream, all the time). We had a daily amount of money ($10 or $15) for her spending money.
One thing I might suggest is letting him take the Pirate Cruise from the GF or take the Family Magic Tour together (we are doing this in March) I have heard wonderful things about them both.
We didn't do commando in any way yet we saw everything (including 15 rides on the Tea Cups and many other duplications). We just took our time and she kicked back in the stoller (maybe he won't go for that, but she was much happier and lasted the whole day - 8-midnight- with energy to spare because she got to ride).
Basically (now that I've gone on forever), just relax and have a GREAT time. Our trip together was my best one ever!