There is no easy way to remove the "outdated" stuff from an existing workspace. Using the "clean" parameter will not really help, as many of the files you refer to are "free form data", only known to the plugins that are no longer available.
Your best bet is to optimize the re-import, where I would like to point out the following:
${old_workspace}/.metadata/.plugins/org.eclipse.core.runtime/.settings
folder from the old to the new workspace. This is surely the fastest way, but it may lead to weird behaviour, because some of your plugins may depend on these settings and on some of the mentioned "free form data" stored elsewhere. (There are even people symlinking these folders over multiple workspaces, but this really requires to use the same plugins on all workspaces.)