Questions
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Is it okay to have different gmail ids for Google plus and Google webmaster tools?
You won't have any issues with this. Most SEO's don't use the same account for webmasters and analytics as they do google+, docs or other things. Google can cope just fine with it. As tom says you can now add users within g+ brand pages and GWT, this is a good way to say these are all connected - you've also been able to do this for a while with analytics.
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