"Trust Layer" might but I think its more for subcontractor COI tracking.

Older buildings likely have nothing but one layer of sheet rock between the floor boards/joists and lower level units.

I'm also not sure if us rehabbing their unit and having them come back to start a new lease in fall would add another layer of complexity.   

If the wiring is nonmetallic cable (romex - plastic looking outside layer of insulation) and has a ground wire (3rd wire, bare copper) it might be fine to keep.

A GC will add another layer of accontability as well. 

I am looking for thoughts on whether I should be proactive with replacing a 20yr+ old roof (missing shingles, multiple layers, looks terrible) and a 25yr+ old hvac.

That distinction is important for one very important reason, the asset decisions are being made by the owners (or a direct family member) which eliminates a layer of defense for all these decisions.

Tax strategy has dozens of layers.

In the kitchens we found up to 7 layers of flooring. 

You are a beginner in REI – so get started first, accumulate some equity, get some serious cashflow going, get some experience with managing real estate, figure out you want to do this long term…and then worry about how to layer an LLC cake.