Run quotemeta on $val, or use \Q$val\E in the regex.

Update: I also had to add a space to the regex: 

s/( [NOR|OR].*.IN1\()(\Q$val\E)( \).*IN2\()([^)]*)(.*)/$1$4$3$2$5/g;
#                               ^

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In reply to Re: Passing a variable to a regex by choroba
in thread Passing a variable to a regex by mavericknik

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