Hello,
We are glad to hear you enjoyed going through the user guide!
For project (3) "Benchmarking and performance optimisation" we suggest you add a new benchmark case to the library to learn how benchmarking works. You can start by having a look at the benchmark/ folder in MDAnalysis, and the related documentation:
For project (4) "Transport property calculations" we suggest that after you learned how to use MDAnalysis, you’ll play with the existing diffusion coefficient calculation module to get an idea how the existing transport code works and what you can use to build on.
Best,
Rocco