Try this:
cd $dir
find ./ | grep "input.txt$" | while read file; do tr -d '\n' < $file | awk '{gsub(/\. /,".\n");print}' | grep “\[" >> SingleOutput.txt; done
This will find all files called input.txt under $dir, the it will perform what you say it's already working send output to $dir/SingleOutput.txt.