@progtesting I am not so familiar with the flat-top version of the microscope. There is a recent thread on the forum from others making it: Flat Top Microscope | IIBM UC | Chile.
The second link you have is for the main microscope in an older version. The current version is linked from the web site at https://openflexure.org/projects/microscope/build and is version 7.0.0-beta1 https://build.openflexure.org/openflexure-microscope/v7.0.0-beta1/. This will not have the parts for the flat-top version.
Edit:
Looking at the links in the flat-top thread, the Gitlab page links to the instructions you have, with the broken links for STLs. However the Gitlab page also has a link to the STLs called ‘the CI artefacts’. That link has a builds folder containing the STLs for 3D printed parts and the DXF for the laser cut parts.