I think I got this idea from @OldEastRR? Anyway had some fun with the table saw and cut down three of the MT over height box cars. I know the shortcomings on these are legion, and I have replaced most of them with newer Atlas and InterMountain offerings. However there are a few paint schemes I wanted to keep. Here is the MT car on the saw, and then next to the Atlas PS-1. Both cars ride on BLMA trucks.
Wow, somebody used my idea! Thing is, that was Method #1, which didn't work out so well trying to get the roof back on. So on the very last MTL conversion I did, I took the extra height off the bottom of the car. The cut went straight acroos the bottom by running through the lower part of the oversized lower door track. The idea is to slice away enough of that track to leave a prototypically thin one. And to continue that cut to both ends of the car. The saw kerf takes care of most of the excess height but careful trimming of the remaining cut-off strip of car (at the top, leave the lower edge untouched) brings the height into line. Then glue the bottom strip of the car side back into place. The guides on the doors need some carefully sanding to let the door open, or wedge it in or glue in place for permanently closed.
I didn't get the cut straight so there are gaps, but those are easier to fill than any on the top of the side. (or cut straight in the first place) You can see how the cut sheared away most of the original lower track. Atlas PS-1 on the right.
There are many advantages to Method#2 over 1: The brakewheel is not affected or damaged, nor the detail around it. No need to try to match the unmatchable color of the MTL car along a top seam. The lower door track now looks right. The end detail of the car is not damaged. This method really isn't too hard since it's much simpler, and anybody could probably correct 2-3 MTL PS-1s in a night.
With both conversions you'll probably need to file down the MTL bolsters a bit to get the correct ride height, but if you did it right the car body should match exactly the Atlas PS-1. I think I had to deepen the recesses inside the car side so it'd sit correctly on the MTL frame.
I meant to write a how-to article about this but I ran out of MTL cars to convert before I decided to.