Cylinder boring without a cylinder borer.

[Toolmaker51]

In my experience, few milling machine configurations have the intrinsic accuracy to bore at depth. Main issue is loss of quill support as it descends from the housing, and instances of swivel heads are rarely as square in 2 planes an indicator reads zero.
That can be improved by tramming with quill extended just shy of the stop, with apparatus to swing a larger diameter along X axis; move Y enough to fall within that range. I use a pair of 1-2-3's and 1 2" jo-block as surfaces, switching axis as needed. Wipe the lower surface on inside of wrist to insure cleanliness.
A lathe has all the accuracy built in, mainly as the part rides well aligned Vee's, quite like a jig bore. And a 5MT indicates a substantial machine. Effectively you were line boring. That is 100% possible if the bar is affixed to the tailstock and a center. Carbide tipped are most accurate, a well lubricated steel center is nearly as good. Live centers are often abused, inducing vibration or like harmonics via dry ball cage and races.
Your solution and dissertation are complete with accurate text and well detailed jpeg's. Those cylinders are so short! I'm guessing RPM range is low or mid 'teens? Is that an intake port in pic #4? Two Stroke and another couple thousand RPM?