What I'd recommend is that you install Bob's mods like normal and go through the process of advancing to the rocket. That'll give you a very solid idea of what the progression is. Then, you will have an idea where you can make your omnimatter recipes available.
Since I haven't played this enough to know how much you've already thought of, I'll withhold further comment at this time till I am more familiar with it. Though the base idea seems pretty sound! It just needs a fair bit of balancing.
