Use webmaster tools "change of address" when doing rel=canonical
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We are doing a "soft migration" of a website. (Actually it is a merger of two websites).
We are doing cross site rel=canonical tags instead of 301's for the first 60-90 days. These have been done on a page by page basis for an entire site. Google states that a "change of address" should be done in webmaster tools for a site migration with 301's. Should this also be done when we are doing this soft move?
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Well, rel=canonical will technically work fine, however in this case if you are migrating the entire site (presuming you have all pages on the old domain, going somewhere on the new domain, I would essentially setup 301 redirects from the old domain to the new domain.
I don't think you should do anything in the webmaster console. Just remove all the pages from the old domain and setup 301s from old domain to new domain. Google Webmaster Console Site migration IMO is for scenarios like you have yourdomain.net and you acquire the domain yourdomain.com and want to migrate the domain from .com to .net or if you change the brand name to yourbrandname.net or so on.
Does that make sense ? I hope that helps.