Update a few references from 3-project-factory to 2-project-factory

[lyricnz]

The move of project-factory from stage 3 to stage 2 #2567 appears to have missed a couple of places

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Checklist

I applicable, I acknowledge that I have:

• Read the contributing guide
• Ran terraform fmt on all modified files
• Regenerated the relevant README.md files using tools/tfdoc.py
• Made sure all relevant tests pass

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[lyricnz]

Looking into tfdoc and removing unnecessary (whitespace) changes.