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These domains previously had ssl certs so I was using the https. The certs made no difference, so I dropped them.
What happens now is that (this is the way apache works) an https connection, when not found for that domain, automatically goes to the first https connection on the server. So when Google is indexing [domain1.com,...] it's actually being served [domain2.com....] Domain2.com has an ssl cert that is being actively used.
What's the best way to clean up this mess? Typically a .htaccess on domain1.com would just 301 to the non https version, but in this case domain2.com is actually being served.
I think in your case you might just want to do a conditional redirect with mod-rewrite to the http version of the site... since 301's should be absolute URLS, in theory there is no problem doing cross domain... don't know if google still has problems with cross-site 301's though - there used to be issues with the original URL being displayed.
pseudocode for mod-rewrite:
REDIRECT [HTTP_DOMAIN...] [R]
If you don't want to do 301's you could always just serve a 404 for those pages.