As someone who is running it on mac here's what I did, I downloaded a pack (BnB for reference), deleted the config, mod, and schematic folders, and then just put in the mod, config, and template folders from ME^3. Then just launching it works fine.
Now for other stuff, I've played a fair bit more and have some more suggestions/thoughts. First the big two, update ME^3 to RC2 and turn on automation please, since otherwise we're stuck with manual synthesis only which is fairly annoying if you actually want to use AE to automate stuff. It also fixes the Keratin glitch. The second big suggestion is to preferably remove the bedrock floor, it just seems distinctly weird for the space station theme, over the void feels like it would look much better.
Is there anyway to fix the mob spawning? Because currently it's overwhelming spiders and dirt creepers with the occasional enderman, I've seen one skeleton ever and no zombies. I have also seen no types of creeper other than dirt creepers, for spiders they are easily 90% desert and pale spiders with baby spiders making up nearly all of the rest. This is just irritating, the mobs feel like they'd be a lot better if it wasn't the same stuff every time, get the skeletons, zombies, and creepers back in.
It's not easy but I'm nearly certain that you could change minechem recipes if you wanted, I could try writing up a little guide thing for you on how to do that if you want? Although currently it seems like you'd need another tiny mod to add decomposing/synthesis recipes and actually modifying the minechem mod to add/remove molecules. It would probably be done some time over the next week if you wanted it, depends on how hard it actually is.