To guide the drilling and get exact dimenions I pre-milled the copper blocks a bit less than the final holes. Putting each copper block next to the other ensured that they will later fit to each other when flipped.

Putting the two blocks together and mounting within a wise, I was able to drill the holes in the exact diameter I needed. After the first hole was drilled, a drill bit was used to avoid that both copper blocks moved while drilling.
Cleaning the holes, tapping screw holes to press both blocks together was the next step for the CPU copper block adapter.
Finally I used a bit of scrap aluminium to make a fixture of teh copper block which I could then screw into the holes of the mainboard for the cooler.
The smaller copper blocks to mount the heat pipes to the alu ribbon cooler I drilled directly which also lead to the loss of one of the drill bits :-)