hi gene- i took a quick look at this today since my never-going-to-go-live portfolio theme already has a custom post type. last night i added some taxonomies to it and this morning i cranked out 12 dummy posts.
so far it looks pretty good. i didn't find anything major. pagination works on the post-type archive page as does the post navigation (next post/previous post). hierarchal and non-hierarchal tags show up.
one thing i think might be missing is a way to get back to say Portfolio type archive if you are at a Portfolio taxonomy archive
Here is a sample post footer:
Portfolio Tags: bacon | Genre: Fantasy | Writer: Jack Whyte | Leave a comment | Edit
If you are at a Portfolio Post then the post footer looks like
Browse the Portfolio Item archive. Portfolio Tags: bacon. Genre: Fantasy. Writer: Jack Whyte. Bookmark the permalink. Trackbacks are closed, but you can post a comment. Edit
Oh and if you are the 'bacon' 'Portfolio Tag' archive then 'bacon' is repeated in the post footer. On regular posts I seem to recall an different footer that said 'Also posted in' or 'Also tagged in' and excluded the tag/cat of your current archive.
That's all I've got so far- Hope it helps some.
and the Portfolio Archive is there.