I have never booked an AP award, so take everything I say with a grain of salt, but:

1) There is a limit to how many segments. I think it's 10? A simple A-B-A via C and D won't run into this issue.

2) Yes, you can call in. They'll then charge a phone booking fee per passenger.

A consideration: from what I can tell, you just want YOW-ATH-YOW. What you can do is go YOW-NYC-ATH-LHR-YOW (which sounds like your new plan?). So I'm not sure where the positioning flight issue comes into play here. It's normal that ap.com doesn't show all options. They want their YQ, after all.

FWIW, I don't think AP.com can book this online, since, iirc, you can only have 3 options under the multi-city search, and your stopover would require there to be four (YOW-NYC, NYC-ATH, ATH-LHR, LHR-YOW)

Again, everything I just said may have been wrong