As a general rule, for section headers, I would favor the briefer forms, such as: Project Description, Project Justification, Project Scope, Benefits, Project Deliverables, Preliminary Schedule, etc.
In an actual sentence, though, either form could be used; for example, either "Here is the preliminary schedule for this project" or "Here is the project's preliminary schedule" would be acceptable.
In an index, you need to take a best guess as to which word the readers will look for when they want to find the information. I would avoid starting any index entry with "Project", as your index would be flooded with entries under the letter P. Instead, I would use a form like this:
Deliverables for the project
Schedule for the project, detailed
Schedule for the project, preliminary
It's not uncommon for an index to list multiple forms for an entry, but usually the page number is only given in one place (this makes the index easier to maintain should new information be added). So, you might consider using something like this, if you feel it would enhance the usability of the index:
Project Deliverables: see Deliverables for the project