I'm probably the worst person to give "cold weather" dressing advice since I live in Minnesota.
Layers are the key. I don't think you'll see any temperatures above 75 that time of year but it probably won't be freezing.
I would leave the flip flops at home unless you want something just to wear up to the pool deck/lido and back to the cabin.
I have cruised Alaska in Septmember and had beautiful weather. Temps in upper 60's and lows in the upper 40's and low 50's. Many people consider this cold. I consider this "cool".
The one thing you really do need to pack is a waterproof jacket or warm jacket and rain poncho. You can be pretty sure that at some point on the cruise it will rain. Nothing will make you colder than being wet.
Jeans are something that you may want to pack but they are heavier.
Don't be afraid to re-wear and/or send out for cleaning. It cuts down on the amount of clothes you'll neeed.
Take care and enjoy the beauty of Alaska.