I'm working on a very similar scenario, where .com.au pages are ranking in Google US and .com pages are ranking in Google AU (above .com.au pages).
We are moving forward with the hreflang attribute since it was specifically introduced to help search engines serve the correct language or regional URL to searchers. In helping search engines index and serve the localized version of your content, “hreflang” also prevents duplicate content penalties by telling Google that each potential “duplicate” is actually an alternative for users who require an alternate language version. * We see this as a short-term goal, as we plan to eventually consolidate the ccTLDs to the .com site.
Here are some international SEO / hreflang resources that might help:
- https://support.google.com/webmasters/answer/189077?hl=en
- http://moz.com/blog/hreflang-behaviour-insights
- http://moz.com/blog/the-international-seo-checklist
- Anything from Aleyda Solis &/or Gianluca Fiorelli
- http://moz.com/blog/using-the-correct-hreflang-tag-a-new-generator-tool
- http://www.themediaflow.com/tool_hreflang.php
Also, since the AU subdomain pages were ranking well, I probably would have left the redirect in place rather than let it go to a 404. Then focus on mapping out the equivalents between the .com and .com.au sites. This is a very tedious project, but the last 2 links I shared above really help move things along once you have all the URL equivalents mapped out.
I hope this helps!
