Did you purchase the 2008 R2 license from an authorized Microsoft reseller They should be your first contact. If you did not purchase from an authorized Microsoft reseller, you might not have a valid copy of software, in which case the only way you could get an activation key for 2003 is to purchase a valid copy of Windows Server.
In the 2003 series of Windows Server products, most SKUs were actually different products. For instance, the OEM Standard Edition and the Volume License Standard Edition were not the same product. Therefore, you couldn't just switch the product key and have everything work. I don't know if the MSDN version was a unique product, but based on the error message you're getting, it seems that it is different from the one that you have a key for. If you received Windows Server 2003 R2 installation media with your new server or the ability to download a matching ISO, what you have to do is perform an operating system upgrade of your Windows Server 2003 R2 installation by using that media. During installation, you enter your new key. This is the only way to switch between Server 2003 Rx SKUs, even if they're the same edition. 153554b96e