martinibuster - 2:10 pm on Apr 12, 2013 (gmt 0)
I just did a server migration, which meant I had to shut the site down first, creating hundreds of thousands of page not found errors, while we changed the DNS settings and then waited over the course of several days for the DNS to change. Disruption in search traffic fun ensued.
The following week we did the software upgrade, again shutting down the site, resulting in hundreds of thousands of pages not found errors. Despite pre-upgrade testing and rehearsals, the actual upgrade did not go smoothly, resulting in an extended downtime of a couple days. THEN we did the htaccess rewrite so that all the link equity of the former pages went to the new URLs. Needless to say, our rankings were in flux as it took another week for the new URLs to work their way through the system. However to compound things, in the middle of URLs getting updated in the search system, Google's own Custom Search Engine updated which resulted in a random code being appended to hundreds of thousands of URLs. Yes, we now had a new set of URLs!
Despite all those hairball inducing events that resulted in the site being down more or less for half the month, traffic and rankings soon returned. So what I'm trying to communicate to you is not to get too caught up in doing many SEO related things for the transition. The less you do the better. The rule of thumb is that the more technical ingredients are introduced the greater the chance that an error will appear. This applies to pretty much any web related project. The simple approach worked for me, despite the transition happening in a stormy manner.
I think here is no need to de-index former pages. In fact, if I understand you correctly, it's possible you'll kill your link equity robot texting the old pages. Although once you start rewriting old URLs to new URLs, old URLs don't technically exist.
I would be much obliged if someone corrected me if I'm in error on any of the above points.