Really those instructions are steering you in the wrong direction. There is no need to build from source code, just use the mojoportal deployment package for MS SQL (not source code), choose the right package depending on whether you have .NET 4 or .NET 3.5, and follow the medium trust instructions.
Typically you should install mojoPortal as a root site or in a virtual folder marked as an application directly below the root.
What you cannot do is install it in a sub folder and then use the crazy GoDaddy url forwarding or url masking or whatever they call it to make it seem like a root site when it really isn't. That is not going to work with mojoPortal.
Hope it helps,