Habitability / break-lease -- need advice, please

[Michael Ten]

Hi! I'm new to the forum (as a poster), but I have enjoyed learning from this community as a lurker. 

I purchased a property through Roofstock in KCMO. It has 1.5 baths on the main floor and a half-bath in the basement. It passed their inspection with no issues, but the inherited tenant complained of plumbing issues in the downstairs half-bath. When she moved out, I had an auger cleaning done as part of the rehab. 

A new tenant moved in on December 1st. On Christmas, she complained of the downstairs toilet backing up, so the property manager sent someone out there. On the 1st, she complained about the same issue again, and we sent out another appliance technician. They flushed the line with a hydrojet and sent a snake in there, and they think there is an obstruction or broken pipe in the system. I have been contacting plumbers to go in, but it requires coordination since the tenant insists on being present, leading to delays. She also just informed me of a roof leak in the garage.

The tenant has withheld rent for January, and she has asked to break the lease early and get her security deposit back. I don't think the relationship can be salvaged, and my property manager is sick of her, too, so I'm happy to see her leave. I understand her frustration, but I view her issues as inconveniences, not an inhabitability issue. I am not inclined to return the deposit in full -- at the very least, taking a pro-rated rent for the 80% of the house that is liveable. 

My question is: do the bathroom or garage situations break the implied warranty, given that the main floor is fully useable, and we have been responding promptly to all requests? Would you return the deposit in full (minus any cleaning costs) and take the hit for January rent? 

Thanks in advance for sharing your experiences!