(These instructions are MOSS 2007, so hopefully they help.)
You can verify that sps3:// is being crawled by looking at your content
sources to ensure that they're configured or your search crawl logs to
ensure that it's actually being crawled. Both of these require you to be on
the "Search Settings" screen in your SSA.
You can check content settings by looking at the content sources defined -
click on the link next to "content sources" under "crawl settings". Bring
up the menu under "Local Office SharePoint Server sites" and click "Edit".
Look at the start addresses for the content source - one of them should be
prefixed by sps3:// or sps3s:// (this should usually also be operating on
the same port as your MySites).
For crawl logs, under "Crawl Settings", click on "Crawl Logs". Your SPS3
connection won't be explicitly listed - you might have to check a few of
those items, since it doesn't list protocol in that list, but again, it's
likely under the same port number as your MySites.