Here are my thoughts.
DO NOT EAT AT CSR!!!! None of the dining establishments at CSR are owned or operated by Disney. I think they're Landry. For somebody with one maybe two common allergies I think they can be fine (depending on the allergy) but for your DS, do NOT even try it. We'll never stay at CSR because we eat a lot at our resort and I do not consider there to be a safe options for us there and we're not as limited as your DS.
I have heard only a few good reviews there for allergies, and a lot of bad ones. I am going to miss our POP chef we had on our last trip.
At MK, with your DS' allergies I suspect that Crystal Palace will be your best bet for the kind of variety of ingredients that the chefs will need to prepare something more than basic rice pasta for him. If he's happy with rice pasta then I would think that Tony's is a great option but otherwise CP should work well. Just be prepared to ask the chef lots of questions because people have either great experiences or else they get this one chef who just doesn't seem to care. I got the latter the one time we ate there but because I know just what questions to ask I was able to keep my kids safe and they still ate pretty well; he eventually clued in to what I would and would not accept and made some simple but safe stuff for them. Even with our experience I have still considered going back because of some amazing reviews that I've read. Just be prepared to ask lots of questions to get a feel for the knowledge of your chef.
After talking to my mom and sister today, we may give up one of the other meals and eat at BOG or even try Cinderella's Castle on the 3rd. That way we don't have to leave the park for a TS meal, and worry about not being able to get back into the park. Have you tried Cinderella's castle? Both places have some type of fish. He will be mostly eating fish that week, and that is why Cape May will not be missed. He can have so much there.
Have you ever eaten at 1900 Park Fare for dinner? That's where you'll find Chef TJ. If you've never experienced Chef TJ then you should really book this ADR. Trust me, you won't regret it.
I have heard so much about him, and would love to eat there one day. Would he be there for breakfast too? Do you think if we ate there for breakfast, we could get to MK before it closes for the day on July 3rd?
CMC - you know is wonderful
Boma - you know is wonderfull; I'm looking forward to trying it for the fist time in February based on the maaaaaaaany great allergy reviews that I've read
50s PTC - I know that lots of people like those "allergy free" milkshakes but I won't order one again here. They do not have a dedicated milkshake machine and not all chefs there are as thorough with the cleaning. My kids both had upset stomaches after eating there last time and I'm pretty sure it was the milkshakes as their symptoms were very much what happens when they get a bit of milk (and it's one of their few common allergies). With lamb and seafood being the only meats he can eat, did you see something on the menu that looks easily modifiable? That would be my biggest concern. Just what do you think they'll be able to prepare for him? They have to have the ingredients in the kitchen in order to customize something for him.
They do have fish on their kid's menu, so he could have that. He won't be able to have all the sides that come with it.
Coral Reef: We've had 2 ok experiences. Everything was safe and well prepared. It just wasn't anything to write home about it. The chefs have a microplaner that they use for grating Enjoy Life chocolate bars over ice cream (I know they have Tofutti and I think they have Rice Dream which is obviously important for your DS if he can't have top 8) for fun sundaes. Because it's a seafood restaurant I would think this is an excellent choice for you. Chef Kim was really good with my kids and knowing that they have those Enjoy Life chocolate bars is wonderful. Our servers left a lot to be desired and basically the chefs were the ones who did everything.
'Ohana breakfast: The menu is limited. Is there enough that he can eat? Can he eat Bob's Red Mill gluten free pancake mix (for Mickey waffles), potatoes and fruit? He can't eat the breakfast meats and eggs from what you're saying. Just make sure that he can eat enough of the foods that they offer. They did a wonderful job for us but we can eat breakfast meats and only one of us can't have eggs and the BRM mix is safe for us. Chefs may be able to go to Kona to get some additional options for him but I wouldn't go assuming that they can as it doesn't always happen (we've never been offered but again my kids can eat plenty there; I've read reviews where people have had this done but again go in assuming they won't).
He was able to eat the allergy friendly waffles when we went when he was 2. He wouldn't eat them though, because he didn't want to eat Mickey. 
He has more allergies now, but I think he can still have Bob's gluten free mix. I will check on that though. Eggs are one of the few top 8 that he can have and most fruits are ok too.
'Ohana dinner: We love this dinner. Your DS can eat all the shrimp he wants though I'll warn you that it's served with the shell on and that shell's sticky and messy. The allergy meal is served over a dish of white rice. They'll also serve steamed broccoli, possibly some crispy rice noodles (we've never gotten them but I know others have) and salad. Depending on who's working, there may be other options but that really is up to the discression of the chef working at the time. My kids get things like non-dairy ice cream and fruit for dessert.
We are all looking forward to this meal!
WCC - We ate there for the first time in August. I got a request to go back. Yup, we liked it. Their allergy corn bread is the BEST. It's made from Namaste and is I believe top 8 free. Since the change to the new menu I don't think I've read an allergy review but I would think that they'd handle things exactly the same way. I just wish they'd do the platter at lunch because we won't eat the lunch foods that actually look like they could be made safe (I can't even remember if there was something that looked like it could be made safe; I just remember being very disappointed when I looked at the new lunch menu and figured we'd never go). We'll likely go back to try the dinner platter. My review is in my signature as a link for August 2012.
