Just sharing a partially solved puzzle for anyone else with my same issue.
If as an admin when you go to your moodle site /admin/tools.php
and you see any missing tools maybe you did what I did: I upgraded from Moodle 2.3 to moodle 2.5 and I found out that in moodle 2.5 some of the tools are missing that WERE in my 2.3 installation. You can tell by going back to the original install folder inside moodle/admin/tools and see if you see the tools there in each version. For me two tools were only in 2.3 not 2.5: bloglevelupgrade and uploadcourses.
So now my question: can I delete them using the delete tool button in tools.php? I assume if 2.5 does not have them anymore they have either been removed or placed somewhere else. Hopefully my mistake can help someone else too!