James,
I'm really glad you got it all working, a couple of comments ...
1. instead of opening the .vbproj file in notepad and moving the files to where the project thinks they are, it's probably better to modify the project to look in your specific location. Once you open the solution in Visual Studio, expand the References section for each project. If any references are incorrect there will be a small yellow yield icon next the the reference. Right click on the 'References' node and select 'Add Reference...'. In the resultant dialog, browse to the location of the missing .dll, select and add it. Do that for each missing reference. When done, all the references will be correct.
2. IF a module is packages properly, you should be able to simply install the 'source' package using the Host->Module Definitions screen. Please refer to each project though to make sure that is the case and see if there are any restrictions, as there are for the Repository which specifies that the source package is for .net 1.1. only.
3. Providing a Nant build file is a personal preference and is not provided with every project. Again, check with the specific project to see if there are any special instructions for re-packaging.
Thanks again and good luck, if you have any further issues or questions just let me know.