I'd call them. AA.com is certainly not behaving well.

1. I'm pretty convinced that the >4 hour layover options are not appearing on AA.com, even though there's a tariff listed according to itasoftware. If you like one of those, they should be able to help out.

2. The further expanded options of AA + American Eagle + American Connection don't show up with the specific radio-button of AA + American Eagle + American Connection, and only appear if you add "oneworld" even though they clearly should appear.

Arrgg. I see why OP is so frustrated.