Thanks for the reply! I've fixed both issues, and I might as well post up how I managed it in case anyone else has the same problems.

No CD: Oddly enough, I found that running the plain GOG version once before over-writing it with the mod .exe did the trick. I'm not sure why, but that's the only difference between the install I did on the laptop, and the one I did on the desktop (I loaded up the GOG version on the desktop once to check the version.)

DirectX error: This I found is caused by missing/incorrectly placed/corrupted spreadsheet files. The chief cause seems to be corrupted or sloppy mods. There are two things that seem to have contributed to fixing this.

First, I switched from the (possibly junk) 1.2.1 Tropical mod I had gotten from MOO Guardian (which USED to be a fantastically reliable source) to the 1.3.1 mod posted by shamusmcfatty here:
[url=]http://www.gog.com/en/forum/master_of_orion/master_of_orion_3_tropical_mod_install_instructions[/url].

Second, and perhaps more importantly, I changed my user permissions. Seems Windows 7 doesn't (by default) allow for winrar to extract to, and over-write files in, the Program Files directory. When I tried, I would get an access denied error each time. Initially, I had just extracted to a non-Program Files folder, then copy and pasted those files into the MOO3 directory. My guess is that when I did this the files weren't applied properly. By enabling full user rights and permissions for the MOO3 folder, I was able to have winrar extract and over-write the files properly, and I'm now happily a few hundred turns into my first game.

Windows claims that each iteration gets more "user-friendly" but I'm finding the opposite to be true. the fact that my administrator account doesn't have the proper rights to mod my games is more than a little annoying :)

Thanks again!