I recommend doing your selects and rough cuts first, then stabilize---if only for memory and performance reasons. You don't want to waste time and other resources stabilizing footage that you're not going to use.
See this for information about memory and storage requirements, leading you to want to stabilize after doing selects and rough cuts:
http://blogs.adobe.com/toddkopriva/2012/05/memory-and-storage-tips-for-warp...
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Todd Kopriva, Adobe Systems Incorporated
product manager, professional video software
After Effects team blog
Premiere Pro team blog
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