Rod,
To machine a casting you have to think like a casting. Bad joke, I know, but only partly in jest. That is a fairly complex casting and as you said getting it set up correctly is critical.
Look at the parting lines on the casting. The main outside shape with the fins has a single main parting line made from the 2 halves of the mold. The inside of the flanged ports on either side probably had separate cores. The cylinder bore also had a separate long core that included the valve pockets, and that core was only supported at one end. As you bored deeper and deeper it got worse and worse. So, the main outside finned halves (which you want to be centered to look nice in the finished model) go together well, but any or all of the cores could be misaligned and not clean-up evenly. That can be typical of some castings.
Here is a way that is time consuming but is accurate, and you generally don't have make much of a machining fixture.
Start by painting all the surfaces that will be machined with machinists blue. Now you need to scribe some lines. You could ( and probably should) start by turning a piece of wood to fit into the bore of the casting. Secure that piece of wood securely, vertically, onto a nice flat surface and set the casting on it. It is best if it fits slightly snug, not sloppy. Now, referencing off the flat surface that wooden post is attached to, check some squarnesses, and things like the flange faces, and the levelness of the fins. Most likely you will find that if the core is vertical, those other features will be tilted. If that is the case, tilt and re-secure the center wooden post to bring the external features into their correct planes, if possible. You said there is a lot of spare metal in the bore, so see how true you can get the outside features without tilting everything too-too much.
Now that the casting is positioned better, touch the blueing up and again scribe some lines where the external machining cuts will be. Once you like how the casting is sitting, you will have to pick some datum surfaces to work from. This is where you can avoid the fixtures. Think how you might position this casting on the mill to take just a few preliminary cuts. Not finish cuts, but instead you will add an equal amount of stock to those 3 or 4 cuts.
So now with the casting still on the wooden post, take an angle grinder and LIGHTLY remove a little material from maybe 3 or 4 small areas to make small surfaces to rest on when you put the part on the mill. If you grind those 3 spots accurately according to your scribe lines and then set it on those points on your mill and clamp it into place on the table, THEN you can take those prelim mill cuts to establish your datum surfaces.
I know this sounds like a PITA, and it definitely is, with all marking and scribing and adjusting and marking again. Castings are seldom very accurate (unless they are investment or other precision casting process) and you want to catch your mistakes with the layout blue, not after you have machined the metal off.
When you are machining those prelim datum cuts you can also machine a few places to clamp on with your 4-jaw, so that you can proceed with some confidence that you know where the finished surfaces will end up.
I know this is long, but it does work.
Lloyd