Pat - I assume the '45 degree' is a typo on your part
You need to establish by maths (CAD) the exact position of entry on the liner of the centreline of the cutter to give the cut off point at .024 below the exhaust as the cutter breaks through. I normally do this from a known edge - eg the lower exhaust flange face or the lower corner after establishing the exact distance from the lower face to the exhaust flange lower face.
Make sure you are absolutely certain of the right place - too low and you can possibly save it but too high and it's a scrapper as far as timing is concerned. Internally it's virtually impossible to measure acurately but you can make simple depth comparisons using a pre set depth guage.
Someone else may have other means to add to this awkward to set up but not too difficult op but that's the way I have gone about it so far
Tug
PS. I have never attempted to broach these holes - a special cutter would certainly need making.
I have Barrete section needle files that I have ground the sides away to fit the hole diameters and file the edges of the transfer ports square but then mine are much larger at 5cc so probably a lot easier to do.
Personally, I would keep as drilled in the first instance and see how the engine runs - the ports can always be tweaked later though you may have to relap the bore and possibly make a new piston after.
another PS.
Regarding positioning, though I have never done it you could scribe a line around the liner at the point of entry and pick that line up with a needle point in the drill chuck to begin with. As said air on the side of caution and be on the lower side of the line rather than above!