To address a couple of things:
1.) I just reinstalled the Mac OS X on my machine to build this configuration with the SSD and additional HHD. Due to the limited space on the SSD (for the money), and the fact that my user folder is very large (I am a software developer and do a lot of graphics and other work as well - all of those files can take up a large amount of space), and generally any app that uses files from that folder never really touches more than one or at most a few of those files at any given time - other than maybe on initial load of the app, I do not want my user folder on the SSD. I am using the SSD for system execution and applications - with very few exceptions. I have no intention of moving my 100GB user folder back onto the SSD. If there is a way to make the game reference a preference file in an arbitrary location, I can set up a location on the boot drive (SSD) to do that. As this is a pretty new install, my permissions should be pretty clean.
2.) When I created/moved the User Folder to the HHD, I told Mac this is where I wanted it - in fact, I had the OS move it. I also created a symbolic link from the old location to the new user folder in terminal in case the standard user folder location was addressed. This should have (in theory, anyway) minimized the problem of locating the file in the new user folder. So, I am not sure why that would be a problem.
3.) I believe I found the preference files for both of the games in the applicable locations, but I did not see any useful information inside those files. And if I remember correctly, the ownership and grouping was correct for each of them - I will have to verify this though as it has been a few days since I have looked at it. I am not sure why the game would not be able to access them.
I hope this answers some of the questions. Again, Thanks for all of the input. Hopefully we can come up with a solution.