Thanks for the advice, turns out I got to much the same place in the end!
After posting the question, I started tinkering and trying version 2. I increased the wall and floor thickness to a full 1mm, and then added a single row of 1mm diameter cross braces to the inside, roughly halfway up the side walls. I also decided to print entirely flat, just to see if it would work.
It did print, but the single row of cross braces, while it improved the walls, did not entirely eliminate the warping. Printing flat also introduced another problem, where the floor seemed to swell somewhat, and the ribs near the ends of the car were warping outwards. I didn't expect that at all! Look at the bottom of the ribs on the car, they are warping outwards the further near the ends. The middle ribs (not seen in the picture) are perfectly aligned! And this only happens when printing flat, completely disappears when printing at even 3 degree angle.
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So back to the drawing board (or, well, tinkercad). I reduced the wall and floor thickness down to .75mm after finding 1mm too thick, and this time I went full lattice bracing!
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This is basically 0.6mm thick square profile bracing, 0.8mm apart. They do not touch the actual floor of the gondola (actually, I find that it prints MUCH nicer if I don't support the floor at all!)
I then printed the same way (upside down) with 5 degree incline. Note that I didn't want to print right-side up because of the suction effect of that large cavity of the gondola would produce. Though I did have two drain holes - 2.1mm diameter holes for the trucks, I have them going right through the floor of the gondola
It printed very nice this time around (finished printing last night, and I cleaned up the print late this afternoon). The only problem I had is I didn't put enough supports, and the top of the walls sagged between the supports. But after sanding down the top of the gondola against a sheet of sandpaper, this is barely noticeable, and easily corrected in my next print by doubling the number of supports around the edges!
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I installed some micro trains trucks, but I have to change them, turns out I need the short coupler, not the medium.
This is what I was trying to reproduce - for copper/zinc concentrate transport:
http://www.rrpicturearchives.net/showPicture.aspx?id=4322869Though please note, I am not really into perfect reproduction of a prototype, I'm happy with "close enough"
Anyway, thanks for the comments, they really are appreciated!