Let me just preface first by saying that I have been enjoying using Shibby's build with the RT-N16 for the past week. I like the built in Transmission client but I noticed that it had no schedule option (besides one that just changes the bandwidth limit). I have read posts about how to schedule downloads using Tomato and they always end up with suggesting disabling QoS altogether or increasing the max limit of incoming traffic. I preferred to rather just increase the % limit for P2P/Bulk and also initialize the built in Transmission client to start it's downloads. This way the downloads will still use up most of the bandwidth at night, yet there will still be some effectiveness of QoS should someone decide to want to use the internet at those hours. I find Transmission easily eating up half of the RT-N16's cpu consistently as well when it's downloading so it made more sense to only run it at night and that way I could keep my computer turned off as well.
Go to Administration > Scheduler. For the first custom script, set the time for when you want to start your downloading with Transmission and increase the P2P % limit. Simply change the ten values with your own QoS's Inbound Class Limits. (if anyone knows of a command to only change the % for one class, please post). The second line simply tells Transmission to start the torrents that it has queued up. For the second custom script, set the time for the downloads to stop and for the P2P % to be reset.
nvram set "qos_irates=10,10,90,90,0,70,70,70,90,1"
transmission-remote -n username:password -t all -s
nvram set "qos_irates=10,10,90,90,0,70,70,70,40,1"
transmission-remote -n username:password -t all -S
It would be nice to see a build with something like this built in.