Hi again Lash151,
I have a confession to make. When I read your original post and you mentioned the side panels being short when you were measuring up for the roof, I believed that you were talking about a difference in height. I also wonder whether some of the other contributors may have thought likewise.
However, as you still seemed unconvinced what to do, I found a side-on picture of 44-020 to see how 'serious' the difference was, and realised that you meant the side panels were short in the lateral dimension not the vertical one.
Consequently, I am going to modify my original response slightly and say, if it were my model, I would alter it, IF, all I had to do was change the side-windows for slightly longer replacements and add a matching extension to the back edge of the side-panels.
Andy