2. The names are user configurable, there are just two needed, one for PNDA application packages and one for archiving data to.
3. The pnda_apps_container and pnda_apps_folder are set in pnda_env.yaml. These values in the YAML do make their way into the salt pillar, but the guide should reference setting them in the yaml not the pillar. You need to create the folder "pnda_apps_folder" ("releases" by default). What goes in here are PNDA application packages (see https://github.com/pndaproject/pnda-guide/tree/master/application, https://github.com/pndaproject/pnda-guide/blob/master/console/applications.md, https://github.com/pndaproject/example-applications).
4. yes github changed their markdown parser, this has been fixed on the develop branch but not ported to master yet.
On next steps, if openstack is all running, you need to create the VM flavours (ec2.m3.xlarge etc) then move onto this step in the guide (https://github.com/pndaproject/pnda-guide/blob/master/provisioning/heat.md)