I really like your right up, and its full of info that so many of use go through on the learning curves with this hobby ( atleast the ones that really dig into the subject).
Your aproach to your little X2 is good IMO. There is a lot to getting any machine to be accurate. and the truth is there is probably not a Asian hobby class desktop machine out there that are really accurate.
YOu have to start from the base so your going in the right dirrection. After all it what all measurements respond to. On your saddle I would go with the class40 iron, the other will work find but the iron willl be easier to work, plus it should give more vibration dampening ( cast iron controlling vibrations is mainly why machines are built from it). Today with better tech in weldments and such we do see many machine not made of iron but they are normally very high tech and expeincive. Then there is the epoxy granite route.
These benchtop machines all go through a seasoning of the casting. This can cause the warping/bending of all the parts even if they where straight to begin with. So heat treating/stress relieving even more will be good. Heck if you dare, or can afford, cyro treating could be a extreeme step to take ( the dovetails & gibs would wear much better then). ABit overkill, but thats what taking it to the next level is about. And by all means go with a tappered gib setup if you go this far, and allow anough room to make the gibs thick enough to hold up and not bend.
Many of the machines get the bases warped/bend from the mounting used when bolted to a bench. Once you get your base fixed make sure you dont kill it again with improper mounting(I am not saying you killed it the first time). Also any improvments you can do to stiffen the castings should be done before cutting & scraping ( epoxy fills, cross supports, added plates and such).
You will learn a lot on this project. And if you get it right you will see just how much a good bearing surface ( scraped ways) really adds to the performance and accuracy of a machine. I giggle when I see machines sold with what they call frosting to add oil retention, and the buyer goes on about how the machine is factory scraped (not). Both are important, but a bunch of random half moons on a way is not scraping. A properly scraped way and saddle will move like it is riding on fluid. It will also have much more stability and accuracy if they are straight. So the performance and speed when CNCed will be much better. Once you master the X2, the RF-45's are just begging for someone to make them into a real machine. My RF-45 is 12 years old and it set for 10 years before even being used. Right from the get go it has problems much like your X2 just from the casting settling/seasoning, and not being setup properly on a bench (it was just stored)
Years ago when I was racing we use to take old engines blocks and throw them out in the weather for a few years. The blocks would change and season at whcih time we would remachine them. They always made for a much stronger, more stable engine after doing such. Its just the nature of cast iron, you either do it to the part through treatments and such, or you let it happen naturally. EIther way the part will always hold its structure much better.
I will be looking forward to seeing how you come on this project, should be interesting.