I'm going to pop in with a question...you mention using his fold-up wheelchair that it seems he doesn't typically use. Is this a standard wheelchair that you have acquired for him since his leg break? Or does he have other reasons for having a wheelchair? I ask because if it's a standard adult sized chair, and not a pediatric chair sized for him, then he really might be more comfortable in a stroller. Most jogging-style strollers have the legs out front rather than dangling below like in an umbrella stroller. At 4 yrs old, he's probably rather small for a standard wheelchair and spending all day in it could get mighty uncomfortable even with a pillow. If the family no longer has a stroller, you can rent one. You would need to get a stroller-as-wheelchair tag and GAC at guest services to be allowed to use the stroller in line (regular wheelchairs are more obvious and don't require a GAC).
As for getting wet, I think a large poncho should cover his leg fine. What does his Dr. recommend regarding rainy days? If it's a very wet day, maybe a trash bag tied on his leg which might allow him more movement (though likely hot!).
As others have indicated, WDW is terrific at handling special needs of all kinds. I'm sure he'll be fine and you'll have a wonderful vacation!