OK, so the custom bike fits you well and informs you of the numbers you want to match. It would seem that you would start with the crank to seat length first, setup the seat for proper knee over pedal next, and then see where you are with respect to the handlebars. If they are off you would approach that with stem and/or bar changes to get close to the right numbers. Once you got it all together you would probably find that the bikes are so different the new one doesn't feel right. Time to see a pro?