Hello all. Thanks for all the advice. Just to be clear...two things: first, I know my site is far from ideally coded, so a lot of this rests on me to fix at a higher level. Second, I think the plugin is great, but perhaps I expected too much (and I know I didn't use it right in the beginning).
First, thanks @djmorrisinc, I never saw the help wizard in the minify section. Again...user error. Just tried it out and on Yslow went from a 55 to 70 with that one tweak!
I still have an issue with having no expires on a lot of content (mainly images). I've set expirations for everything in the browser cache section, but that doesn't seem to do anything. Should I be doing something different?
Last, I was using Cloudfront for nearly everything, but mostly images, but had to turn it off. I found that in IE every image was fine, but in Chrome and Safari some images were missing. There was a box outline where the image should be and when you click on it, the correct image opens in a new tab (so the URL is correct), but for some reason these browsers don't render the image. I'd say it happens with 1 in 20 images and I can't figure out any pattern. Some are old images that I had in place before the plugin and some are new that I've added since. Again, everything is correctly on the cloudfront CDN and so are URLs, but it's not rendering correctly in those two browsers. Any thoughts?
Thanks to everyone for their help. Still a lot more work for me to do, but this plugin and all of your help have done a ton.