Update:
Just to report, 10.9.2 and Server 3.0.3 didn't fix my issue of AFP/SMB users not being disconnected properly. I have found that making users (or forcing them) to shut down thier machines at night does indeed disconnect them in server. Also, I had the server re-starting every night automatically.
If they put thier machines to sleep instead of shutting down, server keeps the connection "alive" showing they are connected. When they come in the next day, it adds another connection for thier account. IPs are the same, and machine are the same. Eventually, between all the times of the day and then at night that their computers sleep, they can end up with 5 or more connections.
I am going to change the idle time and disconnect idle in terminal as my next attempt to fix. I will report back.