Originally Posted by
gemac
Edited to add: OP is correct about the upgrade, I believe. AA's computers treat this as a non-stop, so they want you in the same seat the entire way. That is why OP also was unable to book a seat on the first leg that did not exist on the second leg. I have no personal experience with this, but it has been reported here repeatedly.
My gf was able to upgrade the LGA-ORD leg of a single flight number LGA-ORD-ACA flight about two years ago. The agent just had to break it into two segments both with the same flight number.