By looking at your 2 examples, why don't you;
[1] loop thru the contents of the 2nd file
[2] compare every individual line of the 2nd file with all the lines in the first
[3] print matched lines to file3
[4] After looping thru all the entries in file2, do a diff between file1 and file_matched
[5] parse the o/p of [4] to file4

Disclaimer: I couldn't script if my life depended on it, so can't really help you with that.