WL is a great place to stay! The 3 of you should love it there.
Your itinerary looks good but I do have some observations:
DHS has several rides that tend to attract long lines: ToT, RnRC, ST, and TSMM. ToT, RnRC, and ST can have relatively short waits in September so these should be OK. However, except at park opening, I don't think I've ever seen TSMM Standby queue at less than 50 minutes (and this was near park closing). 90 minutes is not uncommon. With you landing at 9:54 AM, you probably will make it to the park between noon and 1 PM. With the park closing at 11 PM for EMH, 10 hours at DHS should be plenty of time in September. However, there's always the possibility that you could spend a lot of time waiting in line, especially at TSMM. By the time you arrive, I wouldn't be surprised if all TSMM FPs were gone. Personally, we only do TSMM when we have a FP but hopefully you'll have a shorter than normal wait. Since it appears to have been about 7 years since your last trip (based on the age of your daughter), I assume you're not familiar with TSMM. It almost always is a long wait, perhaps longer than anything you've experienced in the past. It's possible that the line could be shorter during Evening EMH, especially once people start queuing up for Fantasmic. Since WDW is offering "Free Dining" in September, it's hard to be sure what crowd levels will be like.
Tuesday morning EMH at Epcot should be good. I assume you plan to head to the World Showcase in the afternoon. Just be warned that if it's a typical September day, it could be hot and humid with afternoon storms. I've always found the World Showcase to be one of the most uncomfortable places at WDW in the afternoon heat.
MK is scheduled to close at 7 PM on Tuesday for Mickey's Halloween Party. Since you have a reservation at Whispering Canyon for 7:50 PM, this shouldn't affect you. (I assume this is why you planned a 7:50 PM reservation.) In fact, it might help since guests tend to avoid MK when it closes early and will give your family a chance to rest for Wednesday's long day at MK.
DAK is a good place to visit for Thursday morning EMH but you might be "done" with the park before your 4:30 PM Rainforest Café reservation, especially since you will be there for the 8 AM opening. It's a good plan though since this should give you time to do nearly everything at DAK.
As you wrote, Thursday evening will be a good time to squeeze in one more visit to your favorite park.