I mark the end of the tang and chamfer it the same way I mark and chamfer the edge before grinding the blade. Gives a sort of "target" to grind to. Since I stop my taper at the back of the bolsters, I just scribe a line there. Does that help?
As to lining up the holes in the scales to be perpendicular to the blade, there are probably as many ways to do that as there are makers.

But my way to do it is to first grind an angle in the end of the scale where it matches up to the bolster. Because I taper from the bolster back, it's not a 90 degree angle there. That is a trial and error process for me, and I just adjust the angle of the table on my disk grinder until I get a no-light match between the scale and the bolster.
Next I superglue the first scale to the tang. Just a drop or two will do it. I learned that trick here and have found it works so much better than the clamps-and-pins method I used to use. Then I superglue a little popsicle stick shim to the end of that scale. It supports the end of the tang just enough to make the centerline of the blade perpendicular to the drill press table, because it's about the same thickness as the steel I've removed from that end of the tang. Then I drill all the holes through that scale. At some point, either before or after drilling, I (try to remember to) use a sharpie to draw around the tang on the scale. That gives me an accurate line to trim the scales to before glue-up, which saves grinding a lot of the scale edge off when I start shaping the handle. Then just popping the edge of the scale against the workbench is enough to break the it off the tang, and I repeat the whole process for the other side.
You'd have to use a shim the right thickness for this to work. I try to taper the tang to a very thin edge at the end of the handle, so the popsicle stick is the right thickness for the 3/16" stock I normally use. I have sanded a bit off the shim at times when the taper isn't as deep as the shim is thick, or when I tapered 1/8" stock. Like Tinker I use slightly oversized drills, which allows a bit of fitup slack, but not so much as you'd see it. (Unless you're using colored epoxy, in which case think that through first.

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I hope this clears it up a little. Again, just my way of doing it.