You have to establish a baseline when it comes to assembly of things like this. Most people use the ricasso or the tang of the knife as their baseline. So first thing, make sure the tang is flat. <.005" flat preferably .001" flat over 5" or so. With a tang that flat, you'll then mate the scale to the tang and will see right way if your scale isn't flat because light will show through. Flattening the scale will give you a nice, uniform fit between 2 pieces, the tang and the scale.
Throwing a bolster into the mix you have to add another degree of constraint in. You start with the same flat:flat relationship between the bolster and tang, but now you must meet up the edges of the bolster to the edges of the scale. This requires the edges of each to not only be flat, but to also be (in this case, where you are not dovetailing) perpendicular to the flat surface. You can do this with a disc grinder, or a belt sander, or a file, or whatever, I find it easiest to accomplish on my disc.
The 3rd degree of constraint comes in when you start plunking holes in. Now the position, form, and orientation of those holes becomes critical to maintaining the surface to surface fit you established. Too much clearance in the scale holes can result in gaps around your pins. Too little clearance for the position and orientation deviation can result in pulling the scale or bolster way from each other. The easiest way to avoid this is to have sufficient clearance in the holes in the tang, and when you drill your second scale, drill it using the first drilled scale as the drill guide, so the holes are put in with the flat surfaces relative to each other and not depending on your drill to be perfectly perpendicular, etc.
Fit and problems with fit begins with flatness.