Its been a couple years since I have ran a league on Yahoo so perhaps my info is wrong, but can't you lock and unlock each team as you want?
You could use a manual waiver system and unlock the #1 priority team to allow one free agent add/drop and then unlock the #2 team and so on...until no one else wants to submit a claim. Then you edit waiver priority accordingly and its FCFS until the season starts.
Another way is also manual...where owners email you the claims in order of preference...then you use waiver priority to sort it out and manually adjust rosters. Once everyone is finished edit the priority for the start of the season and allow FCFS.
Couple ideas...hope they help