hello,
for the first issue, it's permissions, by default the permissions won't be very user friendly..
in the host, create one dir per user, and mount that as the /home/<user>
if the user is already created check the documentation and use the user group
if the user is not created, use gid/uid like this:
config.vm.synced_folder "12cR1", "/media/sf_12cR1", :mount_options => ["dmode=775","fmode=775","uid=54320","gid=54321"]
For the 2nd problem, What will be quicker for you? mount say host www as /var/www ?
other way, is you can use sed, and modify DocumentRoot in /etc/httpd/httpd.conf and then do a restart. you can execute this with a shell script from Vagrantfile
Let me know if you have questions, or need something a bit more detailed.
Alvaro.