2. How are you referencing your css and js files? You need to make sure to reference them such as:
For JS -
<script src="/CMSPages/GetResource.ashx?scriptfile=%7e%2fCMSScripts%2fcustom%2fjqModal.js"></script>
For CSS -
if stylesheet is in General tab
<link href="/CMSPages/GetResource.ashx?stylesheetname=CoorporateSite" type="text/css" rel="stylesheet"/>
if stylesheet is in Theme tab
<link href="/ourworldtours/CMSPages/GetResource.ashx?stylesheetfile=/ourworldtours/App_Themes/CoorporateSite/css/jqModal.css" type="text/css" rel="stylesheet" />
or simply have your "Site" in the SiteManger using your Site CSS Stylesheet. That will generate the stylesheet references for you.
4. Are you saving your files to disk? By default Kentico saves them in SQL.
Output Caching is always very helpful, just make sure you are aware of it. It can be a pain when wanting to update the site.
I like to setup a ping for the site to keep the site in a ready state so it doesn't "go to sleep" and require a compile on the next request.