I may be misunderstanding your question, but when you say
now I cannot contact rim with pad even if I turn the set screws fully in.
it makes me wonder if you have somehow got a pair of normal (short-pull) brake levers for your linear (long-pull) brakes. Some brake levers I have seen even have two positions for the cable end - one for normal and one for linear pull.
Just another thing to check if you haven't already.