Could you provide specific examples of what rules you don't like in the B5 game? I agree that Mongoose's editing has not been the greatest, but scanning over the rules I saw no major problems. (Note: I haven't actually played the game yet).
I do like the D20 Modern rules (except for their non-lethal combat rules), but am wondering if it's worth all the effort to convert. If D20 Future was out, then a lot of the work would already be done. (Another alternative would be to use the rules from D20 Traveller - there's a similar level of grit involved, although the space mechanics and tech levels are slightly different).
Also, how is the Earth Alliance Fact book, if you remove the Nationalities section? I agree that it seems to be in poor taste. But what about details about the colonies, the nation blocks, history, government structures, technology, etc? Are the stats for the Earth Alliance spacecraft any good? Since Bruce Graw wrote the B5 Wars game, I imagine they're pretty solid, unless quality control issues got in the way again.
Best of luck on your retrofit. I'll keep an eye out for future updates.