What variety and type are you growing? You only take out the side shoots on tomatoes which are indeterminate ie they would just go on and on growing in all directions if you don't (I think that's what they are called) For determinate and bush types you don't need to take out the side shoots although it is a good idea to limit the number of stems somewhat or you get problems with crowding and poor air circulation. Cherry types such as Sakura which I grow in my tunnel will go on ripening a few fruit into December if you let them - they pook pretty scruffy by then.
I remove lower leaves (deleafing) when they start to turn a bit yellow or faded, so when they are no longer really effective at photosynthesis - this lets air circulate. Only remove leaves below trusses, not ahead of them.
When you remove side shoots and leaves be very careful to snap them off cleanly as any wounds may let in diseases, rots and blight.
You would stop the top growth when you estimate that any new flowers would not have time to develop and ripen before the end of the season - this depends of course on the size of the fruit.