I would really like a solution to this. Hopefully the SP mod will solve these issues. 
As you've been one of the SP Mod alpha testers (though very naughtily customising it), you know very well that it does.
Apart from the save game issue Jimmy mentioned above, which he and Defiant have been valiantly trying to fix, the SP Mod project is fully playable mission game with all new ships, hardpoints, crew models, yadda yadda, plus NanoFX. I recently fired it up for first time in ages on new quad core rig and, yup, it's stunning to look at.
I'm quite happy to give any advice (that I can recall) for anyone wanting to do their own custom SP from scratch, but in all honesty my advice would be for folks to wait for release as we'll have done all the hard work for you
