I'd agree with Martin, use hardened dowel pins rather than make them. For the plain holes I'd probably use a chucking reamer in a collet. But experiment first on an offcut. Reamers are a bit hit 'n' miss when it comes to fine fits.
Last night I used a 1" slot drill to "drill" a 1.4" deep hole in my cylinder casting ready for the governor valve. The resulting hole measures 1.001" according to my internal micrometer. Fine for my application, but not much good for a precision fit. So I wouldn't use a slot drill in this application.
If I was going to be a perfectionist I'd make a D-bit, do a trial and cylindrically grind the D-bit as needed to sort out the last few tenths.
Long ago I designed a fixture plate for the Tormach/Bridgeport of similar size to the OPs. I bought the jig plate …… but never got around to making the plate. I don't miss it in the least. I hadn't thought about it for ages until this thread appeared.
I can't find the CAD model and drawing I created. But I'm pretty sure the tapped holes were through and the plain holes had a small through hole. I alternated tapped and plain holes along each row, offset by one space between rows.
Andrew