What areas of 1st floor sheetrock sould be replaced subsequnet to a major 2nd floor water leak?
To answer the specific question, you should replace any sheetrock that has mold.  A one-time leak for a day won't cause this -- significant mold arrives when an organic material stays wet for an extended period of time (weeks or more, usually) so you should make sure it's dry before it's repaired.

The bigger problem is what is being covered up.  You need to know what was the cause of the leak and be convinced that it has been corrected properly.  You need to check what you can see for any blackness (i.e. mold).  If you find more than a couple dots, then there are moisture problems beyond this one major leak and the ceiling and walls need to be removed until the full extent of the problem is known and removed.  Don't do this yourself!  Contact a professional remediation company.

Same for the floor.  A one-time thing, even this big, won't cause mold as long as it is fully cleaned up and allowed to dry out completely.  This can be difficult if the water has gotten beneath the surface as it certainly will with carpet, hardwood, etc.; you may have to remove everything down to the subfloor, let it dry, and re-install.

The brown water is a concern.  If it was waste water, then you may have a health hazard and you'll need an environmental assessment.

I understand that this is not property you own, which makes getting this done difficult.  I suggest you do what investigation you can, consult with an unbiased professional, and talk politely with the landlord about your concerns.  If you're not satisfied with the answer, you can take your concerns to the government (mold and waste water are health hazards) and find a new place to live.