Using the bittorrent client called transmission you can setup a cron job to start and stop at the right times of day.

If your on a recent installation of ubuntu you will already have transmission installed so it is only a matter of telling it when to start and stop.

open a terminal window and run

crontab -e

Paste the start and stop lines

#####This line starts transmission at 1:10am
10 1 * * * env DISPLAY=:0 /usr/bin/transmission

#####This line stops transmission at 9:55am
55 9 * * * env DISPLAY=:0 /usr/bin/transmission -q

then press ctrl+o and then ctrl+x to save and quit crontab

Now you can use transmission like you normaly would and then close it and be sure that it will run  overnight and stop within the time period.