Discussing what Aaron wanted, he discovered another difference.
The KCS sample shell has a much smaller exhaust than the regular production SD50. Knowing this, the Kato exhaust does not seem so large.

Time to start a hole.

My guide is the front edge of the stock exhaust.

Aaron wanted the gap to be smaller, so I trimmed the edges a bit.

The first task was to get the basic width toward the front (left). This is all a very slow process so as not to make the hole too big. The goal is no filler.

I squared up the edges on the left side.

The front edge fits. I do not want to cut it any wider.

I have a good ways to go in the back.

I need to file toward the back, but I do NOT want to make the hole wider. So I strategically use my minifile. Here are two identical files- opposite sides.
One edge is smooth and one is serrated.

Here, I'm filing toward the rear of the loco, but my file has the smooth side against the side edge. That way there will be no additional cutting at that edge.
Then I'll flip the file and work on the other edge.

OK. I'm starting to get the front to back width correct. Getting closer. Work SLOWLY and check, check, check.

Because there may be an orientation issue with this part, I make sure I'm working in the same direction by adding a little dot. The dot is away from me (nose to the left).

Ooooo. I'm getting so close. I'm working in microns now.

I true-up the corners on the left side, now I see I need to true up the right side. This is where I use a triangular file to get a sharp edge in the corners. I'll eventually use a #11 Xacto knife in the corners, but only when i'm REALLY close.

I finally got the exhaust in, but I'm not satisfied. It's rotated clockwise a bit.

So I flip the part so the dot is near to me. And that looks better.

Not perfect (to my eye) but it looks much better. I work it to get the right height before I glue it in.

The exhaust sticks up just a little like the prototype.

That's enough for one day!