How do you build stuff?
I was talking to a machinist/toolmaker guy I have known for many years the other day, and we got off on the tangent of what is the best way to build things like one off modifications to vans in our case, or hotrods in his case currently. It really applies to most everything you would make, though.
I tend to not build parts to dimension, for the most part, in that I don't try to accurately locate and drill or tap holes in two different pieces to get them to line up and locate properly in use. I will, instead, roughly locate the holes in one piece, and then transfer them to the other piece after holding them in the finished position I want. He tends to not like transferring holes, and is really good at measuring and getting things to fit properly, but it is a lot of time and work to do.
I do think that the procedures used for transferring holes is very important to get the best results, though, especially when the hole sizes are different in the two pieces, or one is tapped.
I use two methods, normally, depending on what I am doing. Most commonly, I will rough locate, centerpunch, and drill finished holes in one of the pieces. I then clamp them together, or if non critical just hold in place, and take the same drill size and go through the top piece and put a drill spot in the center of the underlying piece ( I find this to work much better than transfer punches). I then use a small pilot drill to pick up the spot and drill through, then drill to size, and/or tap the hole. If I hand held, I finish one hole completely and bolt through before doing the other holes. This works very well in areas that are very hard to layout and measure, like locating holes on the van frame, avoiding the welds, seams, and other holes already there, as the holes can be put in wherever you want them.
The other method is similar, and I only use it for through holes of the same size. I will center punch where I want the holes in the top piece, clamp them together, drill a pilot hole through both pieces, located by the center punches, and then drill out to size. If you unclamp after pilot drilling, you can do the different holes sizes or tap if you want. I don't use this method much any more, as it is more time consuming and entails drilling deeper, small holes.
Of course, all of this is for one off stuff. If there are multiples that are the same, I would make all of them identical, and to dimension.