You really should not worry about your web2.0s showing up on crawlers as long as google has them indexed.
You should allow time for your rankings to move, for some keywords it could take a few days for others it could take several weeks.
It is not really recommended to interconnect all of your sites but if you do have to do so, it would then be better to not automate. Doing it manually would be a better option as any software or plugin will have to go on all domains making it a common factor.
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