Can I set up google analytics to track a number of unique users who completely disengage (don't visit the site at all) on a 90 days period?
There is a dropoff analysis report in Google Analytics which you can use but as with all other GA reports it is anonymous. The GA terms actually state that it is a violation to attempt to identify users based on GA records which are meant to be anonymous. The best way to do this and still stay compliant would be to setup a last accessed field in your database for each user and each time they log into the site add the datestamp. Then you can simply run a scheduled task regularly to run a query and get a list of users who haven't accessed the site in over 90 days and then you can do whatever you need to with the data, this would be completely compliant with GA.