Hey John...just wanted to reply as best I can to your question. While I do not have a child with autism, I am a teacher, and have had a great deal of interaction with preschoolers and grade-schoolers with autism. Along with that has come many classes on child development (not that I know more than anyone else, just want to give my 2 cents).

I would have to say that the flapping you describe can be displayed (and often is) in a normal toddler, at times when he/she gets excited. Just my opinion here, but for what it's worth, my little boy (who is now 3) had delayed speech, and a couple of other signs that worried me a little. Now that he's 3, though, and is so much more aware of his surroundings, I no longer worry. So, I said all that to say, your little one may turn the corner at 3, or your suspicions may be confirmed. It's pretty common for little ones at that age to have pronunciation problems or to display quirky actions that go away as fast as they came like stuttering, repetitive behavior, or even tics (habits) , and if you're like me, any little action will be picked apart when you're suspecting autism. I think you're doing all the right things, as early intervention is key, if it's only a speech problem, or if it's something along the spectrum of autism.
You're a wonderful dad! I'll be praying for your little one. Please keep us informed.