Correct signal analysis flow (Wind Turbine vibration)?
I think the question as is, is unanswerable, but here I am making an attempt of correct it with these comments as answer.


  Should I upsample before or after rectifying?


For the algorithm, if you are finally assessing against a threshold in magnitude, you should not care about down|upsampling. Do not add that.


  Does this process look correct?


Strictly speaking, you are taking the algorithm from your document. Since your document has 200 pages, this is someway hardly to say if you are taking correctly the approach taken by the author. 


  Should I do another LP filter to "clean" up the signal?


This depend on the specific fault you want to capture for the bearing mechanics. From there, you can decide which frequencies to focus, and how to assess them.


  Should I do another LP filter at a lower cutoff frequency to "clean" up the signal?


Again, please check specifically how your algorithm is built. Once you have it implemented, we could study modifications or alternatives.