I am considering buying Independence war for one major faction, The old Buda5 mod which converts the game into a Babylon 5 themed Space Combat sim. Also, I-War appears to be a great game ^_^ Atleast according to your reviews.

So, would this old mod:
http://mods.firstones.com/buda5/iwar/index.html

Work with the GoG Version of the game?

It should work - the GOG version isn't fundamentally different from the original release, apart from the compatibility fixes, and the intro movie playback.

I picked up a B5 based sim a couple years ago called: Babylon 5: I've Found Her (I think). You might look and see if that is still around. I remember it being pretty similar in feel to Iwar.