I feel like if I file a dispute I'll lose any good will and the working relationship I have with the contractor, but on the other hand I feel like if I don't file a dispute I might be out of that $4,000.

Relationships, trust, and goodwill are the reasons a lot of these folks will jump in with you.Now, it does get easier with experience.

We are totally open to keeping the cash in the bank as a show of goodwill, but don't want to keep ALL of it in there FOREVER. 

Resist the urge to start with a gesture of good will lets say when they are late on their rent etc - that means you failed their test.

Take advantage of the opportunity to add a monthly pet fee along with your regular rent increase.Refund the pet fee as a good will jesture and move forward with the higher rent.

Hey @John-David Hails...sounds good....will take you up on that I am sure. 

It could save you the hassle of going thorough litigation or, if this does go to court, buy you tons of goodwill by showing the judge/jury you did everything you could to avoid this issue. 

I think the pictures are pretty good. Will

A little can go a long way with good Will.

His home in Riverside, CA was vacant and in bad condition and there was a title issue that I helped him clean up.Well all this good will has paid off, he came to town for our closing and he asked me exactly what I do.