When I did that radial roof NP car, I started with an Intermountain reefer that was fully assembled and decorated.
If you look at page 3 of that thread (
https://www.therailwire.net/forum/index.php?topic=36214.30)
you can see that I took the ends and roof off and then stripped the sides down to bare gray.
I used Polly S Easy-Lift-Off. I just brushed it onto the car sides, waited a half hour, then brushed away the paint under warm soapy
water. I think I had to do it twice to get them really clean, scrubbing with a soft toothbrush.
The sides and roof on IM cars practically pop off by themselves. They are not glued on very well. In fact, when I got them off,
I could see that they seem to paint the core and then glue these parts on, so the glue is just adhered to the paint (which is
probably why they come apart so easily).
Anyway... there's an option for you. Pop the sides and roof off... then strip the sides, then you can paint which the sides
or roof or ends however you like and glue them back on. I didn't have any problem getting the sides off without breaking the brake wheels or ladders.