Yes I too would like to install a 'clean' Portal without thousands and thousands of items/content already in my Portal.
I am unsure how much of it really is needed.
I am developing a process that may work. Install portal but before you run initial site set up you need to truncate the items and contents files.
...\portal\framework\template
* replaced index.zip with the empty_index.zip
* la_content.zip - emptied the zip
* portal_content.zip - emptied the zip
I ran the site create, no content was in the site but when browsing postgre database with PGadmin found all the tables had records for users/items/content, etc...
** I found data.sql in the templates folder also that inserted all these records.
I truncated the data.sql file as well.
For the most part the Portal is now empty without all the pre-loaded content.
You can also hide the 'Organization' tab by some simple added javascript, so that once the page loads you simply hide the tab so the user never sees it. It's there but not accessible. To share items with the organization as a whole, simply have a new group called 'organization' or 'all' and put everyone in it. I'm still tweaking where I should put the script but it does do the job. I'm sure the same thing could work for the 'gallery' link also.