The good news is that the entire place was sanitized and tested after it was flagged but they never applied to have the flag released.

You should have immediately had someone on this to PROPERLY extract, clean, and sanitize the area before placing air movers and/or dehumidifier to thoroughly dry the area.

We use the Lysol laundry sanitizer.

If it were me, I'd look into the possibility of renewing the lease with  an added charge for basic cleaning and then contract with a cleaning company to come in every week or two weeks to maintain sanitation/safety.

Removing ink requires dabbing with alcohol or hand sanitizer.

City of Chicago sent a violation notice for garbage overflowing…As a landlord and former resident of the property, I know the tenants don’t necessarily are responsible for this. Building next to mine always has tenant...

Often leading to sanitation issues and safety issues, including poor egress and fire hazards.

They also left a bunch of construction items in the patio, which the sanitation department does not discard.  

If trash and recycles are sorted out incorrectly you get hit with a $100 (up to $300) fine from the sanitation department each time.

Our company also provides welcome gifts similar to those you have mentioned – trash bags, hand sanitizer, dish towels, etc.