No copy of the key, she is a carryover tenant from the previous LL who was horrible at managing.
Yes, she can withhold rent of up to $125- with written notice- so long as it is applied to repairs and she can prove it.
The issues are just old windows...I have seen far worse ones, but aside from lead paint hazards, these were weather tight for what they were. The roof leak caused staining and damage on about 8 square feet of wall. It has been addressed, but still leaked last storm and the roofer is coming again.