Another thing:
I notice the reversed printing of "Santa Fe" on the lead unit. I know this is because the skin only includes one side, and it is mirrored on the model. In this case, you actually do want it to be mirrored, because of the warbonnet (not to mention all the little doors and grills). The only thing that needs to flip is the text.
There are two ways to deal with this. One would be to squeeze the opposite side into the skin file, and remap the skin coordinates in the triangles descriptions accordingly. This would mean reducing at least some of the regions in the skin file to a lower resolution, in order to clear up some space. As the side of a diesel engine is pretty big, you'd have to clear up a lot of room; my suggestion would be to "squish" it either vertically or horizontally, let's assume vertical. Then, you've got left and right sides stacked on top of each other in the skin file, both squished to half height. This will make future editing difficult, though not impossible. Next, you have to find the two triangles that make up the left side rectangle, and remap their coordinates, moving the bottom points up by half. Do the same for the right side's triangles, moving the top points down by half. The end result is a loss of resolution in the vertical direction, but it may be tolerable.
The second way I can think of is possibly more involved. It is basically a variation of the CargoIcon feature that freight cars use. If you look at the default boxcar, it is just a brown box with minimal lettering. In the game, though, it shows an icon of whatever it is carrying. This is a "decal" of the cargo's icon, on a rectangle that hovers just in front of the car side. We could add a feature like this to an engine, by adding 8 points (4 each side) which are the same as the corners of the sides I mentioned above, except with a slightly greater X-value (like 3.26 versus 3.25). Then, define two new triangles each side to create the rectangles. You've just created a "decal" layer that is just above the engine's side. Now, what you need to do is map that decal layer to a region of the skin file where you have only the text or logo (anything you don't want mirrored). Naturally, this means locating a region where you can do this, and if the skin file is already chock full then you're back to my first suggestion, as you have to resize something and remap in order to fit it in. The benefit to doing things this second way, though, is that it is more flexible - you'll end up with a skin in which you can choose which things are symmetrical versus which are not. In you Santa Fe case, only the words "Santa Fe" would go onto the decal region.
Here is my trick for remapping skin coordinates:
The coordinates in the 3DP file are all "percentages", i.e. they go from 0.00 up to 1.00, with 0.00 being the top or left sides, and 1.00 being the bottom or right sides. Assuming your image editor gives you feedback on where your mouse cursor is (i.e. you are at pixel 64,152), what you can do is resize the image to a useful size, like 1000 x 1000 pixels. Then, as you mouse over a pixel, you can readily convert it in your head - in this case, pixel 64,152 on a 1000 x 1000 image is really 0.064,0.152 for the 3DP.
Another trick:
If you're hunting for the right triangle to remap, you can find it by trial and error. In the first part of the triangle descriptions, where the three points are listed (like point 08, 09, and 0A), just change one of these points to any other point (like 01, 09, 0A). Load the model in-game, and look around for a warped triangle; you've just changed one corner of a face to a whole different point on the model, so there should be a triangular "hole" somewhere. Obviously, if you can make an educated guess then it will be much easier to narrow things down. But this is essentially how I go about figuring out which points to edit on a model - just change one value to an errant value, then examine the model for the error. Incidentally, if you need to rotate the skin as it is mapped onto a triangle, just change the order of the points in this declaration section. For instance, (09, 0A, 08) is a rotation of (08, 09, 0A); you don't have to change the skin coordinates below. And, to mirror image, you need both triangles that make up the rectangle, then swap pairs of points. For instance, if the second triangle is (0B, 09, 0A), then your four points are 08, 09, 0A, and 0B. By examining the coordinates for X and Y values corresponding to each of these points, you may be able to determine that 08 and 09 share the same X values, as do 0A and 0B. This means 08 and 09 are the left side of the rectangle, while 0A and 0B are the right. We already can deduce that 08 and 0B are at diagonally opposite corners, since they are unique to the two triangles, but you can also just examine the Y values to determine that 08 and 0A form the top while 09 and 0B form the bottom. It helps to just sketch out a rectangle and write all these down - I go through many sheets of graph paper as I work! Now that you know all of this, to flip it all you have to do is swap 08 for 0A and 09 for 0B, and vice-versa. By just changing the calls to the point numbers, you don't have to get into the more difficult coordinate remapping.
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