To elaborate on what Chet said,
I too have never been apart of any event where they stopped the clock to balance tables. Only when redrawing is the clock ever stopped.
When to redraw:
Redraws
Players will have a redraw as determined by the Tournament Director. Generally a redraw will occur either at 1 table out of the money, at 3 tables remaining or when the money is reached.
27 players (Flop), 21 players (Stud), 18 players (6 handed NLH), 15 players (Draw).
There may be a redraw at 2 tables and again lastly at the final table. When the final table is reached there is a redraw for the button.
For the last part of your post:
If you have two tables remaining and need to move one player, you have to wait until the hand is finished before you take the player. If this takes a few minutes, do you add that time again
No, there is no need to add time to the clock.