To make a guide , use either square or round stock, what ever will fit inside what you are drilling. Drill/ream/bore to suite the drill you are using. After drilling through the 1st, then put the guide into place. You will needs shims and clamps to support, or else you make a external packer to support it. You will know when it is correctly aligned as the drill will spin freely. Then drill the next hole and repeat.
Another way is to make a hinge drill jig. Like it says, it is a piece that had been drilled though and cut away or made up of segments like a door hinge,1 side only. The drill goes through the 1st hole of the hinge, the ist drilled hole is in the space, the drill goes through the second hinge hole as a guide, the last gap is where the part is being drilled.
It all depends on your drilling set up etc as to how it can be achieved. Long centre drills can be easy 0.1mm off centre.
Neil