Question:

"I am currently trying to download the Prism software and am getting an
error downloading the dotnetfx.exe file (an Error occurred while
downloading the file
http://www.installengine.com/dotnetfx/dotnetfx.exe). Is this something
you can provide some assistance with thanks."

You can download .Net 2.0 from:
http://www.microsoft.com/downloads/details.aspx?familyid=0856eacb-4362-4b0d-8edd-aab15c5e04f5&displaylang=en

After .Net 2.0 is installed (Restart might be required) you can install Prism.

 Question:

"I have tried to install the software Prism desktop software several times. Each time I receive an error 1603: Error installing Microsoft(R) .Net Framework."

Seems to be a Microsoft issue, here is a possible solution :
http://forums.microsoft.com/WindowsHomeServer/ShowPost.aspx?PostID=3332279&SiteID=50

I also find the following link which worked as well. You might like to have a look at it.
http://turbotax.intuit.com/support/kb/installing/errors/5193.html