One common issue when working with creating new project in Vault and Plant 3d is that the pipe specs that the project uses are from the stock specs instead of the project template that is used in Vault.
The core issue is that when the wizard process can't find specs in the project locally, then it pulls the specs from the installation directory. To identify whether you have specs from a project locally, expand the pipe specs node. Specs that are on your local machine have a grey circle (1), while specs that only exist in Vault have no icon (2).
The fix is to open your Vault project template and pull the specs down is to right-click on the Pipe Specs node, and check out all of the pipe specs and then check them back in. Alternatively, you can right-click each spec and view in the spec viewer if you don't want create a new version when you check them in.
After you have made sure to have local copies of specs in your project template, you can use the project wizard and point to the vault project template. The new project will pull from the copies of the specs on your local machine.