You are assuming incorrectly that creating external runtimes only involve new content.  Many individuals upgrading versions of Poser frequently link their old runtimes to their new programs.  What you really need to decide is how to organize your content.  Your old runtime folder is already organized to some extent with the files within their proper folders.  For example, you may want to create a V3 Clothes runtime.  Create your runtime folder within the 'V3 Clothes' folder and transfer those content specifically designated to dress V3.  Include Geometry and texture files because your content will search for these items when you access them.

I would suggest that you take an inventory of exactly what content you own before undertaking massive transfers.  Assess what is important and use regularly (i.e., models) and delete everything else if you still have your original zip or installer files.  By cleaning house this way, you really start fresh with trimmed down runtimes.  Create a special projects folder and install content that will only be used once or twice and deleted afterwards.  It is good practice to think about your needs for a particular project rather than installing everything you own and then regret that you can't find anything within a very slow program