I have tried everything I've seen online but cant get anywhere.

Unfortunately, you don't show what code you've tried to do these things, so we can't help you with the specific problems you had - we're happy to help you learn if you show your efforts (= code). Here are a few general hints:

• Always Use strict and warnings
• See "open" Best Practices
• See the Basic debugging checklist
• See perlintro
• Note that @yes_finally = <IN> will read the entire file into the array, leaving nothing left for the following while($in = <IN>).
• If you want to sort the words in each line, then yes, you'll need to use split.