Don't know how I missed this thread.
How do you know the exhaust ports on the head are planar? If you are not going to do the head then you might help or hurt the exhaust manifold fit.
Since I don't read anything in the thread about doing the head, I assume that isn't in the plan. Therefore, before I touched the exhaust I'd check the fit between the two. Just put them together with no gasket and use feeler gauges. You might be pleasantly surprised to find out how well it fits. Or you might discover it's worse than you anticipated looking at the manifold alone and your simple job just got a whole lot more complicated. But better to know than not.
Assuming there is nothing in the way, you can also use a straight edge on both parts.
If you really have to do this yourself, I am in @Dabbler
's court on how to flatten it. I think you will probably be disappointed in how a milling job turns out even with a big mill table. But just for the record, I personally recommend bringing it to a good engine shop. It's peanuts in the big picture. Many of those shops will do it in exchange for a donation to their coffee fund or some cash on the table.
My two cents for what it's worth.