This will make for a very nice setup when you get done. Its hard to beat the versatility and durability of one of these mills. The true is it doesnt take much more room fro a full size mill compaired to a bench top mill, the weight and being able ot get into most peoples hobbie shops is what holds most people back form going this route.
AS far as the cleanup, I would not use any sand paper or or such products on it in any way. Even scotch bright is not good. The naval jelly is good and just using something like the green scuff pads that are made for house hold cleaning ( not sctoch bright type). Brass wool also is good. The sand products and the scotch bright can leave bad stuff inbeaded in to the cast iron which willl be a bad thing in time. It may seem like you can clean after using such products like sand paper but cast iron is bad for having micro pores which can hold such particals and cause bad wear later on. Really the little soap filled grean pads like buy for cleaning pots and pans works great, and so does the BRASS wool. The brass wool is real good because it can kinda leave a polished look to the metal, plus its soft enough not to dig in and remove to much metal.
When I cleaned my mill up I did this with three in one oil and the green house hold pads. I soaked the oil on th ebad spots to let the rust soften and then it came right off. Soap and hot water after the scrubing, then oil it all up and it should be good to go.
If the machine has been sitting where it can draw moisture bearings can get rust spots in them. Not much you can do about if they have except replace them ( my spindle did this but it sit a long time after being brought over on a boat, so it had salty moisture). Just run anything you start up slow and give it time to show any heat if there are problems to start up. Rough sound, and heat will be your indicator of any such problems. Running slow speeds at first might save you from a total lockup if anything like this is going on . Using a infra red temp gun can help monitor things like the spindle when you first start it up.
Remember to check the drive screws for rust and oil also. It might be a pain to do so but a total tear down might be best of the table and saddle. Its something you will have to do in time anyway if goign CNC and you will get to know your mill better this way, and maybe again save damaging something that just needs cleaned to last instead of grinding it to death because of unknown hidden rust/dirt.
The old oil should be removed because it will be bad for drawing moisture. Unhooking all the lines at the last point and flushing the system will be will worth the effort. The oil pump if it has drawn moisture and gained rust should be torn down and honed. This could save it from damage also and these things are not cheap. Chances are it is fine, but if it has rusted any as soon as you pump it the seals will destroy abd any rust will be mashed against needed seal surfaces. A tear down could save it.
I know it all sounds like a lot of work, but you need to know how all these system are designed and built anyway. And the money saved, and performance gained will be worth it.
These are nice mills and I wish I had the room and resources to get one myself. Keep us posted on your work and cleanup.
Also be very carefull with your electrical, there is a lot of power goin here. Big capasitors can still be holding lots of joice that will be no fun to get unload with ( can even kill you).
Think about everything your doing, take your time. This big stuff is nothing ot be getting in a hurry with.