The OEM customization guide is in fact a good place to start. It provides an overview of modifying simple things like the CSS, images, etc. Adding a mass of code in front of BI Launch Pad's JSPs isn't so much SDK development as it is altering the templates that drive BI Launch Pad. Sure, you could tweak them. But the reality is there is complexity inherent to maintaining this with each patch you apply to BI4 along the way.
That said, the least invasive you can make it, the better. I'd strongly encourage that per the already recommended OEM customization guide, you start with simple graphic/text swap as appropriate and leave the more invasive stuff out unless you do in fact have a Java-savvy resource in your organization.