i know the problem that you are describing. in stohlman's book on making leather cases, he shows a toiletry bag for men. they are basically made from leather pieces that are "c" shaped but different sizes. yet, when sewn together, they mate up without puckers or pinches.
in a nutshell, i don't know how to figure out what the dimensions need to be to make these two parts come together. you might have to make templates out of paper and do a trial and error thing.
so, i know what your dilemna is, but i can't help (he says as he's pounding his head on the desk).