For the overworld pallettes, you should just be able to re-do them with two instances of LM open. Open the non-custom music rom in one LM, and the custom music rom in the other, then open the overworld editors, and the pallette editors. Then just copy the colors over, number by number.
And the same can be said about Mario's poses, you just need the two roms in separate folders, then extract both's gfx, and look at the Mario tilesets in a GFX editor, then redraw. It'll be tedious, but easier than looking for incorrect poses in playtesting.