First time I went to Orlando it was the first week of September for 5 days: it was miserable. Very hot, very humid and daily showers in the afternoon. Being there for only 5 days I went commando to the parks and came back happy but very tired and said "never again in September".
However I went back in September last year (second and third week) and it was wonderful!
I was very lucky, it rained only once in 15 days for 1 hour only, but the main difference was how I toured.
It will be hot, it will be humid and it will rain. But crowds will be very low (I barely used FPs, more for the sake of trying the FP+ that were still a novelty) so touring the parks can be much more relaxing.
I would suggest: go very early in the morning for rope drop. Tour the parks during the morning when it's cooler. Plan a sit down restaurant for a late lunch (ideally after 12:30) so you can rest in air conditioning when temperatures are very high outside. Then go back to the resort and enjoy the pools or take a nap. You'll recharge your energy and avoid the parks when they are more crowded and hot. After the afternoon shower (if any) go back to a park for a quick dinner and the evening entertainment. You'll have big chances that the afternoon rain has cleared the park and it will be even less crowded.