Is there way to set the torrent on pause by Id and resume it again?
Other clients allow to set torrent on pause for completed and for uncompleted torrents.
Not at the moment. You will have to remove the .torrent from the watched directory, but that also removes its entry. Support for pausing torrents will require some work. Essentially you have to be able to stop most of the supervision tree in and around a torrent to make it pause.
It was implemented (and merged) using fast resume by me.
I think, it should be tested.