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I have seen the same thing for one of my clients. They were ranking page 1/2 for 2 different keyword terms and now they are not in the top 50. Other keyword phrases did not move as much. I am looking around to see what happened or if there was some sort of update...
100% agree on the 301 redirect strategy. The best execution is to 301 redirect each page to the new page on the new site. If you have a TON of pages and can not create a 301 redirection rule for every single page you should at least 301 redirect the proper directories to each other.
One thought is...since you will be doing this 301 redirect why not make the NEW urls user/keyword friendly? Also maybe build some directory structure to the site. Hopefully you will be doing his but just thought I should mention it.