do not know the law in your local area.

But in general, I will not worry about this.

1) they can not put lien on your current house if they have nothing to do with your house like repair, tax, mortgage... 

2) it is possible that they can ask for rent for rest of lease term.  The question is their legal base.  If they did not mention that when you move out, and you can argue that it is a mutual agreement.  Obviously, they did not sent you the bill before they threaten you.

From what you wrote, I can feel that you are very easy (especially extra $100 for pipe) and they want to take adventage of you.  They want to threaten you with impossible lien on your house.  This shows their weekness.  Keep that letter for your future court arguement to show their dishonesty and greedy nature. 

If I were you, I will keep all the paper work, letters and receipts/ used checks.  And I will not respond to them at all.  They would quit if they were smart enough.