Many users face a very similar issue with the speed of their SE site, 3rd party companies have created plugins which can help the speed of your site by combining scripts together.
One Company which provides a plugin to do this is YouNet
Minify plugin empowers your SE website to stream faster by removing unnecessary white space and comments, reducing HTTP requests and JS/CSS bandwidth. SE websites therefore is improved by optimizing the loading time. With Minify plugin, SE website will run faster and smoother, and users will be happier.
By combining scripts can be a good thing as only one script will load helping to reduce the load time, but combining the scripts can also cause a few issues like notification feed not loading when click as its already run on page load.
These are the Settings which will cause you the most issues as you combine all scripts which SE Run on.
These settings will help the Speed of SE and also not cause you problems with the day to day running of SE.
As you are combining the JS scripts and also not changing the order of the loading JS scripts, processing functions like News Feeds Auto Loading, Update Feed will work now with these settings.