My advice would be to look for sed man pages. Also here: http://www.tldp.org/LDP/abs/html/
A simple line to replace text using sed would be: sed -i 's/this/tothis/' file
Now ask for input: read variablename
So basically your script would look like:
echo "Enter filename: "
sed -i 's/KH/K/g' $filetowork
sed -i 's/GG/G/g' $filetowork
This should work but it's untested, test it in safe place first.
The first line is important since it tells which script to use to execute it, also remember to make the script executable with chmod +x, otherwise you should type: sh yourscript.sh