Sometimes a painting has to sit with you awhile before you see what is wrong with it. Plus the second pic never photographed correctly and it was over saturated with bright paint.
I finally got a moment to recreate the clouds on the top pic. I didn't capture the actual look that day because the clouds were really vertical in the sky as if they were shooting upwards. Instead I made them to be more suiting for the actual scene. I also toned down the light with a a very light glaze of liquin and ultramarine blue. I think I am happier with it now.
I still think I need to tweak Bogart's image, next time.