Jen, I used an exacto knife to cut my old cracked rubber from around the glass on the rear glass on my 80 240.... I used black auto silicone from a large tube in a caulking gun and sealed it up... two tubes... like $20 total...
Sealed it up perfectly..... I would get an inch of water on the right side before I did that....
On the creaking....go and find a ' gallon' can of 'ru-glide' ... I think it is just dilute muratic acid... add the proper amount of water into the can... and use the attached tube and sprayer to reach under the car and spray your creaky rubber.... presto, Noise Gone ! And will keep the rubber around longer than just letting it dry up....